bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small G proteins in peroxisome biogenesis: the potential involvement of ADP-ribosylation factor 6
Authors: Anthonio Erin A , Brees Chantal , Baumgart-Vogt Eveline , Hongu Tsunaki , Huybrechts Sofie J , Van Dijck Patrick , Mannaerts Guy P , Kanaho Yasunori , Van Veldhoven Paul P , Fransen Marc 
Published: August 2009

Abstract

Background
Peroxisomes execute diverse and vital functions in virtually every eukaryote. New peroxisomes form by budding from pre-existing organelles or de novo by vesiculation of the ER. It has been suggested that ADP-ribosylation factors and COPI coatomer complexes are involved in these processes.

Results
Here we show that all viable Saccharomyces cerevisiae strains deficient in one of the small GTPases which have an important role in the regulation of vesicular transport contain functional peroxisomes, and that the number of these organelles in oleate-grown cells is significantly upregulated in the arf1 and arf3 null strains compared to the wild-type strain. In addition, we provide evidence that a portion of endogenous Arf6, the mammalian orthologue of yeast Arf3, is associated with the cytoplasmic face of rat liver peroxisomes. Despite this, ablation of Arf6 did neither influence the regulation of peroxisome abundance nor affect the localization of peroxisomal proteins in cultured fetal hepatocytes. However, co-overexpression of wild-type, GTP hydrolysis-defective or (dominant-negative) GTP binding-defective forms of Arf1 and Arf6 caused mislocalization of newly-synthesized peroxisomal proteins and resulted in an alteration of peroxisome morphology.

Conclusion
These observations suggest that Arf6 is a key player in mammalian peroxisome biogenesis. In addition, they also lend strong support to and extend the concept that specific Arf isoform pairs may act in tandem to regulate exclusive trafficking pathways.
Evolutionary rate patterns of the Gibberellin pathway genes
Authors: Yang Yan-hua , Zhang Fu-min , Ge Song 
Published: August 2009

Abstract

Background
Analysis of molecular evolutionary patterns of different genes within metabolic pathways allows us to determine whether these genes are subject to equivalent evolutionary forces and how natural selection shapes the evolution of proteins in an interacting system. Although previous studies found that upstream genes in the pathway evolved more slowly than downstream genes, the correlation between evolutionary rate and position of the genes in metabolic pathways as well as its implications in molecular evolution are still less understood.

Results
We sequenced and characterized 7 core structural genes of the gibberellin biosynthetic pathway from 8 representative species of the rice tribe (Oryzeae) to address alternative hypotheses regarding evolutionary rates and patterns of metabolic pathway genes. We have detected significant rate heterogeneity among 7 GA pathway genes for both synonymous and nonsynonymous sites. Such rate variation is mostly likely attributed to differences of selection intensity rather than differential mutation pressures on the genes. Unlike previous argument that downstream genes in metabolic pathways would evolve more slowly than upstream genes, the downstream genes in the GA pathway did not exhibited the elevated substitution rate and instead, the genes that encode either the enzyme at the branch point (GA20ox) or enzymes catalyzing multiple steps (KO, KAO and GA3ox) in the pathway had the lowest evolutionary rates due to strong purifying selection. Our branch and codon models failed to detect signature of positive selection for any lineage and codon of the GA pathway genes.

Conclusion
This study suggests that significant heterogeneity of evolutionary rate of the GA pathway genes is mainly ascribed to differential constraint relaxation rather than the positive selection and supports the pathway flux theory that predicts that natural selection primarily targets enzymes that have the greatest control on fluxes.
Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: Conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss)
Authors: Phillips Ruth B , Keatley Kimberly A , Morasch Matthew R , Ventura Abigail B , Lubieniecki Krzysztof P , Koop Ben F , Danzmann Roy G , Davidson William S 
Published: August 2009

Abstract

Background
Most teleost species, especially freshwater groups such as the Esocidae which are the closest relatives of salmonids, have a karyotype comprising 25 pairs of acrocentric chromosomes and 48–52 chromosome arms. After the common ancestor of salmonids underwent a whole genome duplication, its karyotype would have 100 chromosome arms, and this is reflected in the modal range of 96–104 seen in extant salmonids (e.g., rainbow trout). The Atlantic salmon is an exception among the salmonids as it has 72–74 chromosome arms and its karyotype includes 12 pairs of large acrocentric chromosomes, which appear to be the result of tandem fusions. The purpose of this study was to integrate the Atlantic salmon's linkage map and karyotype and to compare the chromosome map with that of rainbow trout.

Results
The Atlantic salmon genetic linkage groups were assigned to specific chromosomes in the European subspecies using fluorescence in situ hybridization with BAC probes containing genetic markers mapped to each linkage group. The genetic linkage groups were larger for metacentric chromosomes compared to acrocentric chromosomes of similar size. Comparison of the Atlantic salmon chromosome map with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in these species, corresponding to entire chromosome arms in the rainbow trout.

Conclusion
It had been suggested that some of the large acrocentric chromosomes in Atlantic salmon are the result of tandem fusions, and that the small blocks of repetitive DNA in the middle of the arms represent the sites of chromosome fusions. The finding that the chromosomal regions on either side of the blocks of repetitive DNA within the larger acrocentric chromosomes correspond to different rainbow trout chromosome arms provides support for this hypothesis.
Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)
Authors: Chaudhary Bhupendra , Hovav Ran , Flagel Lex , Mittler Ron , Wendel Jonathan F 
Published: August 2009

AbstractBackgroundReactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in growing cells. Because ROS are important to cell growth, ROS modulation could be responsive to natural or human-mediated selection pressure in plants. To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes ("fibers") of cotton (Gossypium), using a phylogenetic approach.ResultsWe measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes in progenitor diploid species revealed significant up-regulation of ROS scavenging and potential signaling processes in domesticatedG. arboreum. Similarly, in two independently domesticated allopolyploid species (G. barbadenseandG. hirsutum) antioxidant genes were substantially up-regulated in comparison to antecedent wild forms. In contrast, analyses of threewildallopolyploid species indicate that genomic merger and ancient allopolyploid formation had no significant influences on regulation of ROS related genes. Remarkably, many of the ROS-related processes diagnosed as possible targets of selection were shared among diploid and allopolyploid cultigens, but involved different sets of antioxidant genes.ConclusionOur data suggests that parallel human selection for enhanced fiber growth in several geographically widely dispersed species of domesticated cotton resulted in similar and overlapping metabolic transformations of the manner in which cellular redox levels have become modulated.
Relationship between estrogen receptor α location and gene induction reveals the importance of downstream sites and cofactors
Authors: Parisi Fabio , Sonderegger Bernhard , Wirapati Pratyaksha , Delorenzi Mauro , Naef Felix 
Published: August 2009

Abstract

Background
To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanisms of target gene regulation by human estrogen receptor α (hERα), we combine extensive location and expression datasets with genomic sequence analysis. In particular, we study the influence of patterns of DNA occupancy by hERα on expression phenotypes.

Results
We find that strong ChIP-chip sites co-localize with strong hERα consensus sites and detect nucleotide bias near hERα sites. The localization of ChIP-chip sites relative to annotated genes shows that weak sites are enriched near transcription start sites, while stronger sites show no positional bias. Assessing the relationship between binding configurations and expression phenotypes, we find binding sites downstream of the transcription start site (TSS) to be equally good or better predictors of hERα-mediated expression as upstream sites. The study of FOX and SP1 cofactor sites near hERα ChIP sites shows that induced genes frequently have FOX or SP1 sites. Finally we integrate these multiple datasets to define a high confidence set of primary hERα target genes.

Conclusion
Our results support the model of long-range interactions of hERα with the promoter-bound cofactor SP1 residing at the promoter of hERα target genes. FOX motifs co-occur with hERα motifs along responsive genes. Importantly we show that the spatial arrangement of sites near the start sites and within the full transcript is important in determining response to estrogen signaling.
Cloning and characterization of a glucosyltransferase from Crocus sativusstigmas involved in flavonoid glucosylation
Authors: Moraga Ángela Rubio , Mozos Almudena Trapero , Ahrazem Oussama , Gómez-Gómez Lourdes 
Published: August 2009

Abstract

Background
Flavonol glucosides constitute the second group of secondary metabolites that accumulate in Crocus sativus stigmas. To date there are no reports of functionally characterized flavonoid glucosyltransferases in C. sativus, despite the importance of these compounds as antioxidant agents. Moreover, their bitter taste makes them excellent candidates for consideration as potential organoleptic agents of saffron spice, the dry stigmas of C. sativus.

Results
Using degenerate primers designed to match the plant secondary product glucosyltransferase (PSPG) box we cloned a full length cDNA encoding CsGT45 from C. sativus stigmas. This protein showed homology with flavonoid glucosyltransferases. In vitro reactions showed that CsGT45 catalyses the transfer of glucose from UDP_glucose to kaempferol and quercetin. Kaempferol is the unique flavonol present in C. sativus stigmas and the levels of its glucosides changed during stigma development, and these changes, are correlated with the expression levels of CsGT45 during these developmental stages.

Conclusion
Findings presented here suggest that CsGT45 is an active enzyme that plays a role in the formation of flavonoid glucosides in C. sativus.
Feasibility of a multidimensional home-based exercise programme for the elderly with structured support given by the general practitioner's surgery: Study protocol of a single arm trial preparing an RCT [ISRCTN58562962]
Authors: Hinrichs Timo , Bucchi Claudio , Brach Michael , Wilm Stefan , Endres Heinz G , Burghaus Ina , Trampisch Hans-Joachim , Platen Petra 
Published: August 2009

Abstract

Background
Physical activity programmes can help to prevent functional decline in the elderly. Until now, such programmes use to target either on healthy community-dwelling seniors or on elderly living in special residences or care institutions. Sedentary or frail people, however, are difficult to reach when they live in their own homes. The general practitioner's (GP) practice offers a unique opportunity to acquire these people for participation in activity programmes. We conceptualised a multidimensional home-based exercise programme that shall be delivered to the target group through cooperation between GPs and exercise therapists. In order to prepare a randomised controlled trial (RCT), a feasibility study is being conducted.

Methods
The study is designed as a single arm interventional trial. We plan to recruit 90 patients aged 70 years and above through their GPs. The intervention lasts 12 weeks and consists of physical activity counselling, a home-exercise programme, and exercise consultations provided by an exercise therapist in the GP's practice and via telephone. The exercise programme consists of two main components: 1. a combination of home-exercises to improve strength, flexibility and balance, 2. walking for exercise to improve aerobic capacity. Primary outcome measures are: appraisal by GP, undesirable events, drop-outs, adherence. Secondary outcome measures are: effects (a. motor tests: timed-up-and-go, chair rising, grip strength, tandem stand, tandem walk, sit-and-reach; b. telephone interview: PRISCUS-Physical Activity Questionnaire, Short Form-8 Health Survey, three month recall of frequency of falls, Falls Efficacy Scale), appraisal by participant, exercise performance, focus group discussion. Data analyses will focus on: 1. decision-making concerning the conduction of a RCT, 2. estimation of the effects of the programme, detection of shortcomings and identification of subgroups with contrary results, 3. feedback to participants and to GPs.

Conclusion
A new cooperation between GPs and exercise therapists to approach community-dwelling seniors and to deliver a home-exercise programme is object of research with regard to feasibility and acceptance. In case of success, an RCT should examine the effects of the programme. A future implementation within primary medical care may take advantage from the flexibility of the programme.

Trial registration
Current Controlled Trials ISRCTN58562962.
Systematic validation of predicted microRNAs for cyclin D1
Authors: Jiang Qiong , Feng Ming-Guang , Mo Yin-Yuan 
Published: August 2009

Abstract

Background
MicroRNAs are the endogenous small non-coding RNA molecules capable of silencing protein coding genes at the posttranscriptional level. Based on computer-aided predictions, a single microRNA could have over a hundred of targets. On the other hand, a single protein-coding gene could be targeted by many potential microRNAs. However, only a relatively small number of these predicted microRNA/mRNA interactions are experimentally validated, and no systematic validation has been carried out using a reporter system.

Methods
In this study, we used luciferease reporter assays to validate microRNAs that can silence cyclin D1 (CCND1) because CCND1 is a well known proto-oncogene implicated in a variety of types of cancers. We chose miRanda http://www.microRNA.org as a primary prediction method. We then cloned 51 of 58 predicted microRNA precursors into pCDH-CMV-MCS-EF1-copGFP and tested for their effect on the luciferase reporter carrying the 3'-untranslated region (UTR) of CCND1 gene.

Results
Real-time PCR revealed the 45 of 51 cloned microRNA precursors expressed a relatively high level of the exogenous microRNAs which were used in our validation experiments. By an arbitrary cutoff of 35% reduction, we identified 7 microRNAs that were able to suppress Luc-CCND1-UTR activity. Among them, 4 of them were previously validated targets and the rest 3 microRNAs were validated to be positive in this study. Of interest, we found that miR-503 not only suppressed the luciferase activity, but also suppressed the endogenous CCND1 both at protein and mRNA levels. Furthermore, we showed that miR-503 was able to reduce S phase cell populations and caused cell growth inhibition, suggesting that miR-503 may be a putative tumor suppressor.

Conclusion
This study provides a more comprehensive picture of microRNA/CCND1 interactions and it further demonstrates the importance of experimental target validation.
Nuclear expression of Snail1 in borderline and malignant epithelial ovarian tumours is associated with tumour progression
Authors: Tuhkanen Hanna , Soini Ylermi , Kosma Veli-Matti , Anttila Maarit , Sironen Reijo , Hämäläinen Kirsi , Kukkonen Laura , Virtanen Ismo , Mannermaa Arto 
Published: August 2009

Abstract

Background
Transcription factor Snail1 has a central role in induction of epithelial-mesenchymal transition (EMT). The aim of the present study was to elucidate the expression of Snail1 protein during epithelial ovarian tumourigenesis and to study the association of Snail1 expression with clinicopathological factors and prognosis.

Methods
Epithelial and stromal fibroblast-like fusiform cells of 14 normal ovarian samples, 21 benign, 24 borderline and 74 malignant epithelial ovarian tumours were studied for Snail1 protein using immunohistochemistry.

Results
Nuclei of surface peritoneal cells of normal ovaries (n = 14) were regarded as negative for Snail1. Nuclear expression of Snail1 protein in epithelial ovarian tumours was increased during tumour progression from precursor lesions into carcinomas both in epithelial (p = 0.006) and stromal cells (p = 0.007). Nuclei of benign tumours (n = 21) were negative for Snail1. In borderline tumours (n = 24) occasional positive epithelial cells were found in 2 (8%) samples and in 3 (13%) samples stromal cells were focally positive for Snail1. In carcinomas (n = 74) focal Snail1 staining in epithelial cells was present in 17 (23%) tumours, and in stromal cells in 18 (24%) tumours. Nuclear expression of Snail1 in epithelial or stromal cells was not associated with clinicopathological factors or prognosis.

Conclusion
Nuclear Snail1 expression seems to be related to tumour progression, and expression in borderline tumours indicates a role for Snail1 in early epithelial ovarian tumour development. Snail1 also appears to function more generally in tissue remodelling as positive staining was demonstrated in stromal cells.
The relationship between physical performance measures, bone mineral density, falls, and the risk of peripheral fracture: a cross-sectional analysis
Authors: Khazzani Hamza , Allali Fadoua , Bennani Loubna , Ichchou Linda , El Mansouri Laila , Abourazzak Fatima E , Abouqal Redouane , Hajjaj-Hassouni Najia 
Published: August 2009

Abstract

Background
Several factors, in addition to low bone mineral density (BMD), have been identified as risks for fractures, including reduced levels of physical activity, poor balance and low physical performance. The aim of this study was to evaluate the relationship between physical performance measures, BMD, falls, and the risk of peripheral fracture in a population sample of Moroccan women.

Methods
484 healthy women were included. Three measures were used to assess physical performance: timed get-up-and-go test 'TGUGT', five-times-sit-to-stand test '5 TSTS' and 8-feet timed walk '8 FTW'. The association between physical performance measures and BMD, peripheral fracture and falls was performed by univariate and multivariate analysis.

Results
The mean age was 55.1 years. Higher 'TGUGT', '5 TSTS', '8 FTW' test scores were associated with lower BMD measured at different sites (p range from < 0.001 to 0.005). The relationship between the three tests and BMD in all measured sites remained significant after multiple linear regression (p range from <0.001 to 0.026). In the group of post-menopausal patients, the scores of 'TGUGT' and '8 FTW' were significantly higher in fractured patients compared with patients without. After logistic regression, a score of 'TGUGT' > 14.2 sec, a score of '5 TSTS' > 12.9 sec and a score of '8 FTW' > 4.6 sec respectively, increased the probability of anterior peripheral fracture by 2.7, 2.2 and 2.3 (OR = 2.7; 95% CI = 1.2–6.4, OR = 2.2; 95% CI = 1.1–5.2; and OR = 2.3; 95% CI = 1.1–5.1). There was a significant positive correlation between the number of fall/year and the 3 tests. This correlation persisted after poisson regression.

Conclusion
This study suggested that low physical performance is associated with low BMD, and a high risk of history of falls and fractures.
Chronic pain in primary care. German figures from 1991 and 2006
Authors: Frießem Christine H , Willweber-Strumpf Anne , Zenz Michael W 
Published: August 2009

Abstract

Background
Until now only limited research has been done on the prevalence of chronic pain in primary care. The aim of this investigation was to study the health care utilisation of patients suffering from pain. How many patients visit an outpatient clinic because of the symptom of pain? These data were compared with data from a similar study in 1991, to investigate whether improvements had been achieved.

Methods
A total of 1201 consecutive patients visiting outpatient clinics were surveyed in six practices in the western part of Germany on randomly selected days by means of questionnaires. Topics were the point prevalence of pain and the period prevalence of chronic pain, its characteristics and its impact on daily life, as well as data on previous therapies for pain. A retrospective comparison was made with the data from a similar study with same design surveying 900 patients that took place in five practices during 1991.

Results
In 2006, pain was the main reason for consulting a doctor in 42.5% of all patients (1991: 50.3%). Of all respondents, 62% suffered from pain on the particular day of the consultation, and 40% reported that they had been suffering from pain for more than six months (1991: 36.4%). As many as 88.3% of patients with chronic pain reported a negative impact on their daily life due to this pain (1991: 68%), and 88.1% reported impairment of their working life because of chronic pain (1991: 59.1%).

Conclusion
Pain, and chronic pain in particular, is a central problem in primary care. Over the last 15 years, the number of patients suffering from chronic pain has not decreased. In nearly half of all cases, pain is still the reason for health care utilisation in outpatient clinics. Pain represents a major primary health care problem with enormous impact on public health. Improvements can only be achieved by improving the quality of health care at the primary care level.