bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis
Authors: Trick Martin , Kwon Soo-Jin , Choi Su Ryun , Fraser Fiona , Soumpourou Eleni , Drou Nizar , Wang Zhi , Lee Seo Yeon , Yang Tae-Jin , Mun Jeong-Hwan , Paterson Andrew H , Town Christopher D , Pires J Chris , Pyo Lim Yong , Park Beom-Seok , Bancroft Ian 
Published: November 2009

Abstract

Background
The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed structure for an ancestral karyotype and models for the evolution of the B. rapa genome by triplication and segmental rearrangement, but these have not been validated at the sequence level.

Results
We developed computational tools to analyse the public collection of B. rapa BAC end sequence, in order to identify candidates for representing collinearity discontinuities between the genomes of B. rapa and A. thaliana. For each putative discontinuity, one of the BACs was sequenced and analysed for collinearity with the genome of A. thaliana. Additional BAC clones were identified and sequenced as part of ongoing efforts to sequence four chromosomes of B. rapa. Strikingly few of the 19 inter-chromosomal rearrangements corresponded to the set of collinearity discontinuities anticipated on the basis of previous studies. Our analyses revealed numerous instances of newly detected collinearity blocks. For B. rapa linkage group A8, we were able to develop a model for the derivation of the chromosome from the ancestral karyotype. We were also able to identify a rearrangement event in the ancestor of B. rapa that was not shared with the ancestor of A. thaliana, and is represented in triplicate in the B. rapa genome. In addition to inter-chromosomal rearrangements, we identified and analysed 32 BACs containing the end points of segmental inversion events.

Conclusion
Our results show that previous studies of segmental collinearity between the A. thaliana, Brassica and ancestral karyotype genomes, although very useful, represent over-simplifications of their true relationships. The presence of numerous cryptic collinear genome segments and the frequent occurrence of segmental inversions mean that inference of the positions of genes in B. rapa based on the locations of orthologues in A. thaliana can be misleading. Our results will be of relevance to a wide range of plants that have polyploid genomes, many of which are being considered according to a paradigm of comprising conserved synteny blocks with respect to sequenced, related genomes.
Gene network and pathway analysis of bovine mammary tissue challenged with Streptococcus uberis reveals induction of cell proliferation and inhibition of PPARγ signaling as potential mechanism for the negative relationships between immune response and lipid metabolism
Authors: Moyes Kasey M , Drackley James K , Morin Dawn E , Bionaz Massimo , Rodriguez-Zas Sandra L , Everts Robin E , Lewin Harris A , Loor Juan J 
Published: November 2009

AbstractBackgroundInformation generated via microarrays might uncover interactions between the mammary gland andStreptococcus uberis(S. uberis) that could help identify control measures for the prevention and spread ofS. uberismastitis, as well as improve overall animal health and welfare, and decrease economic losses to dairy farmers. The main objective of this study was to determine the most affected gene networks and pathways in mammary tissue in response to an intramammary infection (IMI) withS. uberisand relate these with other physiological measurements associated with immune and/or metabolic responses to mastitis challenge withS. uberisO140J.ResultsStreptococcus uberisIMI resulted in 2,102 (1,939 annotated) differentially expressed genes (DEG). Within this set of DEG, we uncovered 20 significantly enriched canonical pathways (with 20 to 61 genes each), the majority of which were signaling pathways. Among the most inhibited wereLXR/RXR SignalingandPPARα/RXRα Signaling. Pathways activated by IMI wereIL-10 SignalingandIL-6 Signalingwhich likely reflected counter mechanisms of mammary tissue to respond to infection. Of the 2,102 DEG, 1,082 were up-regulated during IMI and were primarily involved with the immune response, e.g.,IL6,TNF,IL8, IL10, SELL, LYZ, andSAA3. Genes down-regulated (1,020) included those associated with milk fat synthesis, e.g.,LPIN1, LPL, CD36, andBTN1A1. Network analysis of DEG indicated thatTNFhad positive relationships with genes involved with immune system function (e.g.,CD14, IL8, IL1B, andTLR2) and negative relationships with genes involved with lipid metabolism (e.g.,GPAM,SCD,FABP4,CD36, andLPL) and antioxidant activity (SOD1).ConclusionResults provided novel information into the early signaling and metabolic pathways in mammary tissue that are associated with the innate immune response toS. uberisinfection. Our study indicated that IMI challenge withS. uberis(strain O140J) elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that were associated with a marked inhibition of lipid synthesis, stress-activated kinase signaling cascades, and PPAR signaling (most likely PPARγ). This latter effect may provide a mechanistic explanation for the inverse relationship between immune response and milk fat synthesis.
In vivo imaging of the tonoplast intrinsic protein family in Arabidopsis roots
Authors: Gattolin Stefano , Sorieul Mathias , Hunter Paul R , Khonsari Roman H , Frigerio Lorenzo 
Published: November 2009

Abstract

Background
Tonoplast intrinsic proteins (TIPs) are widely used as markers for vacuolar compartments in higher plants. Ten TIP isoforms are encoded by the Arabidopsis genome. For several isoforms, the tissue and cell specific pattern of expression are not known.

Results
We generated fluorescent protein fusions to the genomic sequences of all members of the Arabidopsis TIP family whose expression is predicted to occur in root tissues (TIP1;1 and 1;2; TIP2;1, 2;2 and 2;3; TIP4;1) and expressed these fusions, both individually and in selected pairwise combinations, in transgenic Arabidopsis. Analysis by confocal microscopy revealed that TIP distribution varied between different cell layers within the root axis, with extensive co-expression of some TIPs and more restricted expression patterns for other isoforms. TIP isoforms whose expression overlapped appeared to localise to the tonoplast of the central vacuole, vacuolar bulbs and smaller, uncharacterised structures.

Conclusion
We have produced a comprehensive atlas of TIP expression in Arabidopsis roots, which reveals novel expression patterns for not previously studied TIPs.
Systematic investigation of gastrointestinal diseases in China (SILC): validation of survey methodology
Authors: Yan Xiaoyan , Wang Rui , Zhao Yanfang , Ma Xiuqiang , Fang Jiqian , Yan Hong , Kang Xiaoping , Yin Ping , Hao Yuantao , Li Qiang , Dent John , Sung Joseph , Zou Duowu , Johansson Saga , Halling Katarina , Liu Wenbin , He Jia 
Published: November 2009

Abstract

Background
Symptom-based surveys suggest that the prevalence of gastrointestinal diseases is lower in China than in Western countries. The aim of this study was to validate a methodology for the epidemiological investigation of gastrointestinal symptoms and endoscopic findings in China.

Methods
A randomized, stratified, multi-stage sampling methodology was used to select 18 000 adults aged 18-80 years from Shanghai, Beijing, Xi'an, Wuhan and Guangzhou. Participants from Shanghai were invited to provide blood samples and undergo upper gastrointestinal endoscopy. All participants completed Chinese versions of the Reflux Disease Questionnaire (RDQ) and the modified Rome II questionnaire; 20% were also invited to complete the 36-item Short Form Health Survey (SF-36) and Epworth Sleepiness Scale (ESS). The psychometric properties of the questionnaires were evaluated statistically.

Results
The study was completed by 16 091 individuals (response rate: 89.4%), with 3219 (89.4% of those invited) completing the SF-36 and ESS. All 3153 participants in Shanghai provided blood samples and 1030 (32.7%) underwent endoscopy. Cronbach's alpha coefficients were 0.89, 0.89, 0.80 and 0.91, respectively, for the RDQ, modified Rome II questionnaire, ESS and SF-36, supporting internal consistency. Factor analysis supported construct validity of all questionnaire dimensions except SF-36 psychosocial dimensions.

Conclusion
This population-based study has great potential to characterize the relationship between gastrointestinal symptoms and endoscopic findings in China.
Diabetes and hypertension markedly increased the risk of ischemic stroke associated with high serum resistin concentration in a general Japanese population: the Hisayama Study
Authors: Osawa Haruhiko , Doi Yasufumi , Makino Hideichi , Ninomiya Toshiharu , Yonemoto Koji , Kawamura Ryoichi , Hata Jun , Tanizaki Yumihiro , Iida Mitsuo , Kiyohara Yutaka 
Published: November 2009

Abstract

Background
Resistin, secreted from adipocytes, causes insulin resistance in mice. The relationship between resistin and coronary artery disease is highly controversial, and the information regarding resistin and ischemic stroke is limited. In the present study, the association between serum resistin concentration and cardiovascular disease (CVD) was investigated in a general Japanese population.

Methods
A total of 3,201 community-dwelling individuals aged 40 years or older (1,382 men and 1,819 women) were divided into quintiles of serum resistin, and the association between resistin and CVD was examined cross-sectionally. The combined effect of either diabetes or hypertension and high serum resistin was also assessed. Serum resistin was measured using ELISA.

Results
Compared to those without CVD, age- and sex-adjusted mean serum resistin concentrations were greater in subjects with CVD (p = 0.002) or ischemic stroke (p < 0.001), especially in those with lacunar and atherothrombotic infarction, but not elevated in subjects with hemorrhagic stroke or coronary heart disease. When analyzed by quintile of serum resistin concentration, the age- and sex-adjusted odds ratio (OR) for having CVD and ischemic stroke increased with quintile of serum resistin (p for trends, 0.02 for CVD, < 0.001 for ischemic stroke), while such associations were not observed for hemorrhagic stroke or coronary heart disease. Compared to the first quintile, the age- and sex-adjusted OR of ischemic stroke was greater in the third (OR = 3.54; 95% confidence interval [CI], 1.17-10.67; p = 0.02), fourth (OR = 4.48; 95% CI, 1.53-13.09; p = 0.006), and fifth quintiles (OR = 4.70; 95% CI, 1.62-13.61; p = 0.004). These associations remained substantially unchanged even after adjustment for other confounding factors including high-sensitivity C-reactive protein. In the stratified analysis, the combination of high serum resistin and either diabetes or hypertension markedly increased the risk of ischemic stroke.

Conclusion
Elevated serum resistin concentration appears to be an independent risk factor for ischemic stroke, especially lacunar and atherothrombotic infarction in the general Japanese population. The combination of high resistin and the presence of either diabetes or hypertension increased the risk of ischemic stroke.
The relationship of Plasmodium falciparum humeral immunity with HIV-1 immunosuppression and treatment efficacy in Zambia
Authors: Van Geertruyden Jean-Pierre , Van Eijk Erika , Yosaatmadja Francisca , Kasongo Webster , Mulenga Modest , D'Alessandro Umberto , Rogerson Stephen 
Published: November 2009

Abstract

Background
HIV-1 infection affects malaria humeral immunity during pregnancy, but data for non-pregnant adults are lacking. This study reports the impact of HIV-1 infection and other variables on the level of malaria humeral immunity in adults with clinical malaria and whether humeral immune suppression was a risk factor for treatment failure.

Methods
Sera of 224 HIV-1 infected and 115 uninfected adults were compared for IgG to merozoite antigens AMA-1 and MSP2 (3D7 and FC27 types) determined by ELISA, and for IgG to the Variant Surface Antigens (VSA) of three different parasite line E8B, A4 and HCD6 determined by flow cytometry.

Results
Compared to HIV-1 uninfected adults, AMA-1 IgG was lower in HIV-1 infected (P = 0.02) and associated with low CD4 count AMA-1 IgG (P = 0.003). Low IgG to all three merozoite antigens was associated with less anemia (P = 0.03). High parasite load was associated with low MSP2 IgG 3D7 and FC27 types (P = 0.02 and P = 0.08). Antibody levels to VSA did not differ between HIV-1 infected and uninfected adults. However, low VSA IgGs were associated with high parasite load (P ≤ 0.002 for each parasite line) and with treatment failure (P ≤ 0.04 for each parasite line).

Conclusion
HIV-1 affects humeral responses to AMA-1, but seems to marginally or not affect humeral responses to other merozoite antigens and VSAs. The latter were important for controlling parasite density and predict treatment outcome.
Study of age-related changes in postural control during quiet standing through Linear Discriminant Analysis
Authors: Cavalheiro Guilherme L , Almeida Maria Fernanda S , Pereira Adriano A , Andrade Adriano O 
Published: November 2009

AbstractBackgroundThe human body adopts a number of strategies to maintain an upright position. The analysis of the human balance allows for the understanding and identification of such strategies. The displacement of the centre of pressure (COP) is a measure that has been successfully employed in studies regarding the postural control. Most of these investigations are related to the analysis of individuals suffering from neuromuscular disorders. Recent studies have shown that the elderly population is growing very fast in many countries all over the world, and therefore, researches that try to understand changes in this group are required. In this context, this study proposes the analysis of the postural control, measured by the displacement of the COP, in groups of young and elderly adults.MethodsIn total 59 subjects participated of this study. They were divided into seven groups according to their age. The displacement of the COP was collected for each subject standing on a force plate. Two experimental conditions, of 30 seconds each, were investigated: opened eyes and closed eyes. Traditional and recent digital signal processing tools were employed for feature computation from the displacement of the COP. Statistical analyses were carried out in order to identify significant differences between the features computed from the distinct groups that could allow for their discrimination.ResultsOur results showed that Linear Discrimination Analysis (LDA), which is one of the most popular feature extraction and classifier design techniques, could be successfully employed as a linear transformation, based on the linear combination of standard features for COP analysis, capable of estimating a unique feature, so-calledLDA-value, from which it was possible to discriminate the investigated groups and show a high correlation between this feature and age.ConclusionThese results show that the analysis of features computed from the displacement of the COP are of great importance in studies trying to understand the ageing process. In particular, theLDA-valueshowed to be an adequate feature for assessment of changes in the postural control which can be related to functional changes that occur over the ageing.
iNOS activity is necessary for the cytotoxic and immunogenic effects of doxorubicin in human colon cancer cells
Authors: De Boo Sara , Kopecka Joanna , Brusa Davide , Gazzano Elena , Matera Lina , Ghigo Dario , Bosia Amalia , Riganti Chiara 
Published: November 2009

AbstractBackgroundDoxorubicin is one of the few chemotherapeutic drugs able to exert both cytotoxic and pro-immunogenic effects against cancer cells. Following the drug administration, the intracellular protein calreticulin is translocated with an unknown mechanism onto the plasma membrane, where it triggers the phagocytosis of tumour cells by dendritic cells. Moreover doxorubicin up-regulates the inducible nitric oxide (NO) synthase (iNOS) gene in cancer cells, leading to huge amounts of NO, which in turn acts as a mediator of the drug toxicity and as a chemosensitizer agent in colon cancer. Indeed by nitrating tyrosine on the multidrug resistance related protein 3, NO decreases the doxorubicin efflux from tumour cells and enhances the drug toxicity. It is not clear if NO, beside playing a role in chemosensitivity, may also play a role in doxorubicin pro-immunogenic effects. To clarify this issue, we compared the doxorubicin-sensitive human colon cancer HT29 cells with the drug-resistant HT29-dx cells and the HT29 cells silenced foriNOS(HT29iNOS-).ResultsIn both HT29-dx and HT29iNOS-cells, doxorubicin did not induce NO synthesis, had a lower intracellular accumulation and a lower toxicity. Moreover the drug failed to promote the translocation of calreticulin and the phagocytosis of HT29-dx and HT29iNOS-cells, which resulted both chemoresistant and immunoresistant. However, if NO levels were exogenously increased by sodium nitroprusside, the chemosensitivity to doxorubicin was restored in HT29iNOS-cells. In parallel the NO donor per se was sufficient to induce the exposure of calreticulin and to increase the phagocytosis of HT29iNOS-cells by DCs and their functional maturation, thus mimicking the pro-immunogenic effects exerted by doxorubicin in the parental drug-sensitive HT29 cells.ConclusionOur data suggest that chemo- and immuno-resistance to anthracyclines are associated in colon cancer cells and rely on a common mechanism, that is the inability of doxorubicin to induceiNOS. Therefore NO donors might represent a promising strategy to restore both chemosensitivity and immunosensitivity to doxorubicin in resistant cells.
The secretions of oviduct epithelial cells increase the equine in vitrofertilization rate: are osteopontin, atrial natriuretic peptide A and oviductin involved?
Authors: Mugnier Sylvie , Kervella Morgane , Douet Cécile , Canepa Sylvie , Pascal Géraldine , Deleuze Stefan , Duchamp Guy , Monget Philippe , Goudet Ghylène 
Published: November 2009

AbstractBackgroundOviduct epithelial cells (OEC) co-culture promotesin vitrofertilization (IVF) in human, bovine and porcine species, but no data are available from equine species. Yet, despite numerous attempts, equine IVF rates remain low. Our first aim was to verify a beneficial effect of the OEC on equine IVF. In mammals, oviductal proteins have been shown to interact with gametes and play a role in fertilization. Thus, our second aim was to identify the proteins involved in fertilization in the horse.Methods & resultsIn the first experiment, we co-incubated fresh equine spermatozoa treated with calcium ionophore andin vitromatured equine oocytes with or without porcine OEC. We showed that the presence of OEC increases the IVF rates. In the subsequent experiments, we co-incubated equine gametes with OEC and we showed that the IVF rates were not significantly different between 1) gametes co-incubated with equinevsporcine OEC, 2) intact cumulus-oocyte complexesvsdenuded oocytes, 3) OEC previously stimulated with human Chorionic Gonadotropin, Luteinizing Hormone and/or oestradiolvsnon stimulated OEC, 4)in vivo vs in vitromatured oocytes.In order to identify the proteins responsible for the positive effect of OEC, we first searched for the presence of the genes encoding oviductin, osteopontin and atrial natriuretic peptide A (ANP A) in the equine genome. We showed that the genes coding for osteopontin and ANP A are present. But the one for oviductin either has become a pseudogene during evolution of horse genome or has been not well annotated in horse genome sequence. We then showed that osteopontin and ANP A proteins are present in the equine oviduct using a surface plasmon resonance biosensor, and we analyzed their expression during oestrus cycle by Western blot. Finally, we co-incubated equine gametes with or without purified osteopontin or synthesized ANP A. No significant effect of osteopontin or ANP A was observed, though osteopontin slightly increased the IVF rates.ConclusionOur study shows a beneficial effect of homologous and heterologous oviduct cells on equine IVF rates, though the rates remain low. Furthers studies are necessary to identify the proteins involved. We showed that the surface plasmon resonance technique is efficient and powerful to analyze molecular interactions during fertilization.
The incidence of juvenile rheumatoid arthritis in Quebec: a population data-based study
Authors: Ehrmann Feldman Debbie , Bernatsky Sasha , Houde Michelle 
Published: November 2009

Abstract

Objective
To determine the population incidence of juvenile rheumatoid arthritis (JRA) in Quebec.

Methods
We obtained data from Quebec's physician claims database. Incident cases were defined as having a visit for JRA in 2000, no visit in the previous 3 years, a confirmed diagnosis by an arthritis specialist, or having ≥ 2 visits to any physician for JRA, ≥ 2 months apart but within 2 years.

Results
Cumulative incidence of JRA was 17.8/100,000. Mean age at diagnosis was 9.8 ± 4.6 years, 68% were female and more persons were diagnosed in winter. Subjects had a median of 10 medical visits over the first year.

Conclusion
Our population based incidence estimate was similar to others. Children and adolescents with JRA are heavy users of medical care. Additional study of environmental or climate- related triggers may be warranted.