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排序方式: 共有110条查询结果,搜索用时 15 毫秒
101.
Nabbe KC van Lent PL Holthuysen AE Sloëtjes AW Koch AE Radstake TR van den Berg WB 《Arthritis research & therapy》2005,7(2):R392-R401
During immune-complex-mediated arthritis (ICA), severe cartilage destruction is mediated by Fcγ receptors (FcγRs) (mainly
FcγRI), cytokines (e.g. IL-1), and enzymes (matrix metalloproteinases (MMPs)). IL-13, a T helper 2 (Th2) cytokine abundantly
found in synovial fluid of patients with rheumatoid arthritis, has been shown to reduce joint inflammation and bone destruction
during experimental arthritis. However, the effect on severe cartilage destruction has not been studied in detail. We have
now investigated the role of IL-13 in chondrocyte death and MMP-mediated cartilage damage during ICA. IL-13 was locally overexpressed
in knee joints after injection of an adenovirus encoding IL-13 (AxCAhIL-13), 1 day before the onset of arthritis; injection
of AxCANI (an empty adenoviral construct) was used as a control. IL-13 significantly increased the amount of inflammatory
cells in the synovial lining and the joint cavity, by 30% to 60% at day 3 after the onset of ICA. Despite the enhanced inflammatory
response, chondrocyte death was diminished by two-thirds at days 3 and 7. The mRNA level of FcγRI, a receptor shown to be
crucial in the induction of chondrocyte death, was significantly down-regulated in synovium. Furthermore, MMP-mediated cartilage
damage, measured as neoepitope (VDIPEN) expression using immunolocalization, was halved. In contrast, mRNA levels of MMP-3,
-9, -12, and -13 were significantly higher and IL-1 protein, which induces production of latent MMPs, was increased fivefold
by IL-13. This study demonstrates that IL-13 overexpression during ICA diminished both chondrocyte death and MMP-mediated
VDIPEN expression, even though joint inflammation was enhanced. 相似文献
102.
Audit B Vaillant C Arneodo A d'Aubenton-Carafa Y Thermes C 《Journal of molecular biology》2002,316(4):903-918
It has been established that the precise positioning of nucleosomes on genomic DNA can be achieved, at least for a minority of them, through sequence-dependent processes. However, to what extent DNA sequences play a role in the positioning of the major part of nucleosomes is still debated. The aim of the present study is to examine to what extent long-range correlations (LRC) are related to the presence of nucleosomes. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. The exploration of a number of eukaryotic and bacterial genomes through the optics of the so-called "wavelet transform microscope" reveals a characteristic scale of 100-200 bp that separates two regimes of different LRC. Here, we focus on the existence of LRC in the small-scale regime (10-200 bp) which are actually observed in eukaryotic genomes, in contrast to their absence in eubacterial genomes. Analysis of viral DNA genomes shows that, like their host's genomes, eukaryotic viruses present LRC but eubacterial viruses do not. There is one exception for genomes of poxviruses (Vaccinia and Melamoplus sanguinipes) which do not replicate in the cell nucleus and do not exhibit LRC. No small-scale LRC are detected in the genomes of all examined RNA viruses, with the exception of retroviruses. These results together with the observation of LRC between particular sequence motifs known to participate in the formation of nucleosomes (e.g. AA dinucleotides) strongly suggest that the 10-200 bp LRC are a signature of the sequence-dependence of nucleosome positioning. Finally, we discuss possible interpretations of these LRC in terms of the physical mechanisms that might govern the positioning and the dynamics of the nucleosomes along the DNA chain through cooperative processes. 相似文献
103.
Olivier Hyrien Aurélien Rappailles Guillaume Guilbaud Antoine Baker Chun-Long Chen Arach Goldar Nataliya Petryk Malik Kahli Emilie Ma Yves d'Aubenton-Carafa Benjamin Audit Claude Thermes Alain Arneodo 《Journal of molecular biology》2013
The Replicon Theory proposed 50 years ago has proven to apply for replicons of the three domains of life. Here, we review our knowledge of genome organization into single and multiple replicons in bacteria, archaea and eukarya. Bacterial and archaeal replicator/initiator systems are quite specific and efficient, whereas eukaryotic replicons show degenerate specificity and efficiency, allowing for complex regulation of origin firing time. We expand on recent evidence that ~ 50% of the human genome is organized as ~ 1,500 megabase-sized replication domains with a characteristic parabolic (U-shaped) replication timing profile and linear (N-shaped) gradient of replication fork polarity. These N/U-domains correspond to self-interacting segments of the chromatin fiber bordered by open chromatin zones and replicate by cascades of origin firing initiating at their borders and propagating to their center, possibly by fork-stimulated initiation. The conserved occurrence of this replication pattern in the germline of mammals has resulted over evolutionary times in the formation of megabase-sized domains with an N-shaped nucleotide compositional skew profile due to replication-associated mutational asymmetries. Overall, these results reveal an evolutionarily conserved but developmentally plastic organization of replication that is driving mammalian genome evolution. 相似文献
104.
Djie Tjwan Thung Joep de Ligt Lisenka EM Vissers Marloes Steehouwer Mark Kroon Petra de Vries Eline P Slagboom Kai Ye Joris A Veltman Jayne Y Hehir-Kwa 《Genome biology》2014,15(10)
Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users. 相似文献105.
106.
K van Oers A W Santure I De Cauwer N EM van Bers R PMA Crooijmans B C Sheldon M E Visser J Slate M AM Groenen 《Heredity》2014,112(3):307-316
Linking variation in quantitative traits to variation in the genome is an important, but
challenging task in the study of life-history evolution. Linkage maps provide a valuable
tool for the unravelling of such trait−gene associations. Moreover, they give
insight into recombination landscapes and between-species karyotype evolution. Here we
used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of
over 2000 individuals to produce high-density linkage maps of the great tit (Parus
major), a passerine bird that serves as a model species for ecological and
evolutionary questions. We created independent maps from two distinct populations: a
captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom
(UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and
1917 cM for the NL and UK populations, respectively, and were similar in size and
marker order. Subtle levels of heterochiasmy within and between chromosomes were
remarkably consistent between the populations, suggesting that the local departures from
sex-equal recombination rates have evolved. This key and surprising result would have been
impossible to detect if only one population was mapped. A comparison with zebra finch
Taeniopygia guttata, chicken Gallus gallus and the green anole lizard
Anolis carolinensis genomes provided further insight into the evolution of
avian karyotypes. 相似文献
107.
108.
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110.
Marieke Biegstraaten Ivo N van Schaik Wouter Wieling Frits A Wijburg Carla EM Hollak 《BMC neurology》2010,10(1):38