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31.
Hilde Nelissen Dominique Eeckhout Kirin Demuynck Geert Persiau Alan Walton Michiel van Bel Marieke Vervoort Jasper Candaele Jolien De Block Stijn Aesaert Mieke Van Lijsebettens Sofie Goormachtig Klaas Vandepoele Jelle Van Leene Michael Muszynski Kris Gevaert Dirk Inzé Geert De Jaeger 《The Plant cell》2015,27(6):1605-1619
Most molecular processes during plant development occur with a particular spatio-temporal specificity. Thus far, it has remained technically challenging to capture dynamic protein-protein interactions within a growing organ, where the interplay between cell division and cell expansion is instrumental. Here, we combined high-resolution sampling of the growing maize (Zea mays) leaf with tandem affinity purification followed by mass spectrometry. Our results indicate that the growth-regulating SWI/SNF chromatin remodeling complex associated with ANGUSTIFOLIA3 (AN3) was conserved within growing organs and between dicots and monocots. Moreover, we were able to demonstrate the dynamics of the AN3-interacting proteins within the growing leaf, since copurified GROWTH-REGULATING FACTORs (GRFs) varied throughout the growing leaf. Indeed, GRF1, GRF6, GRF7, GRF12, GRF15, and GRF17 were significantly enriched in the division zone of the growing leaf, while GRF4 and GRF10 levels were comparable between division zone and expansion zone in the growing leaf. These dynamics were also reflected at the mRNA and protein levels, indicating tight developmental regulation of the AN3-associated chromatin remodeling complex. In addition, the phenotypes of maize plants overexpressing miRNA396a-resistant GRF1 support a model proposing that distinct associations of the chromatin remodeling complex with specific GRFs tightly regulate the transition between cell division and cell expansion. Together, our data demonstrate that advancing from static to dynamic protein-protein interaction analysis in a growing organ adds insights in how developmental switches are regulated. 相似文献
32.
Van Leene J Boruc J De Jaeger G Russinova E De Veylder L 《Trends in plant science》2011,16(3):141-150
Although protein-protein interaction (PPI) networks have been shown to offer a systems-wide view of cellular processes, only a few plant PPI maps are available. Recently, the core cell cycle of Arabidopsis thaliana has been analyzed by three independent PPI technologies, including yeast two-hybrid systems, bimolecular fluorescence complementation and tandem affinity purification. Here, we merge the three interactomes with literature-curated and computationally predicted interactions, paving the way for a comprehensive picture of the plant core cell cycle machinery. Platform-specific interactions unveil the strengths and weaknesses of each detection method and give insights into the nature of the interactions among cell cycle proteins. Moreover, comparison of the obtained data reveals that a complete interactome can only be obtained when multiple techniques are applied in parallel. 相似文献
33.
Introduction
Anti-Ro antibodies can be found in the serum of the majority of patients with Sjögren''s syndrome (SS). Immunization with a 60-kDa Ro peptide has been shown to induce SS-like symptoms in mice. The aim of this study was to investigate factors involved in salivary gland (SG) dysfunction after immunization and to test whether the induction of SS could be improved.Methods
Ro60 peptide immunization was tested in Balb/c mice, multiple antigenic peptide (MAP)-Ro60 and Pertussis toxin (PTX) were tested in SJL/J mice. In addition, two injection sites were compared in these two strains: the abdominal area and the tailbase. Each group of mice was tested for a loss of SG function, SG lymphocytic infiltration, anti-Ro and anti-La antibody formation, and cytokine production in cultured cells or homogenized SG extracts.Results
Ro60 peptide immunization in the abdominal area of female Balb/c mice led to impaired SG function, which corresponded with increased Th1 cytokines (IFN-γ and IL-12) systemically and locally in the SG. Moreover, changing the immunization conditions to MAP-Ro60 in the abdominal area, and to lesser extend in the tailbase, also led to impaired SG function in SJL/J mice. As was seen in the Balb/c mice, increased IFN-γ in the SG draining lymph nodes accompanied the SG dysfunction. However, no correlation was observed with anti-MAP-Ro60 antibody titers, and there was no additional effect on disease onset or severity.Conclusions
Effective induction of salivary gland dysfunction after Ro60 peptide immunization depended on the site of injection. Disease induction was not affected by changing the immunization conditions. However, of interest is that the mechanism of action of Ro60 peptide immunization appears to involve an increase in Th1 cytokines, resulting in the induction of SG dysfunction. 相似文献34.
O-acetylation of cryptococcal capsular glucuronoxylomannan is essential for interference with neutrophil migration 总被引:3,自引:0,他引:3
Ellerbroek PM Lefeber DJ van Veghel R Scharringa J Brouwer E Gerwig GJ Janbon G Hoepelman AI Coenjaerts FE 《Journal of immunology (Baltimore, Md. : 1950)》2004,173(12):7513-7520
The capsular polysaccharide glucuronoxylomannan (GXM) of Cryptococcus neoformans has been shown to interfere with neutrophil migration. Although several receptors have been implied to mediate this process, the structural perspectives are unknown. Here, we assess the contribution of 6-O-acetylation and xylose substitution of the (1-->3)-alpha-d-mannan backbone of GXM, the variable structural features of GXM, to the interference with neutrophil migration. We compare chemically deacetylated GXM and acetyl- or xylose-deficient GXM from genetically modified strains with wild-type GXM in their ability to inhibit the different phases of neutrophil migration. Additionally, we verify the effects of de-O-acetylation on neutrophil migration in vivo. De-O-acetylation caused a dramatic reduction of the inhibitory capacity of GXM in the in vitro assays for neutrophil chemokinesis, rolling on E-selectin and firm adhesion to endothelium. Genetic removal of xylose only marginally reduced the ability of GXM to reduce firm adhesion. In vivo, chemical deacetylation of GXM significantly reduced its ability to interfere with neutrophil recruitment in a model of myocardial ischemia (65% reduction vs a nonsignificant reduction in tissue myeloperoxidase, respectively). Our findings indicate that 6-O-acetylated mannose of GXM is a crucial motive for the inhibition of neutrophil recruitment. 相似文献
35.
A goodness-of-fit test for multinomial logistic regression 总被引:1,自引:0,他引:1
This article presents a score test to check the fit of a logistic regression model with two or more outcome categories. The null hypothesis that the model fits well is tested against the alternative that residuals of samples close to each other in covariate space tend to deviate from the model in the same direction. We propose a test statistic that is a sum of squared smoothed residuals, and show that it can be interpreted as a score test in a random effects model. By specifying the distance metric in covariate space, users can choose the alternative against which the test is directed, making it either an omnibus goodness-of-fit test or a test for lack of fit of specific model variables or outcome categories. 相似文献
36.
Effects of Lactococcus lactis on Composition of Intestinal Microbiota: Role of Nisin 总被引:1,自引:0,他引:1 下载免费PDF全文
Nete Bernbom Tine Rask Licht Carl-Henrik Brogren Birthe Jelle Anette H. Johansen Iker Badiola Finn K. Vogensen Birgit Nrrung 《Applied microbiology》2006,72(1):239-244
This study examined the ability of (i) pure nisin, (ii) nisin-producing Lactococcus lactis strain CHCC5826, and (iii) the non-nisin-producing L. lactis strain CHCH2862 to affect the composition of the intestinal microbiota of human flora-associated rats. The presence of both the nisin-producing and the non-nisin-producing L. lactis strains significantly increased the number of Bifidobacterium cells in fecal samples during the first 8 days but decreased the number of enterococci/streptococci in duodenum, ileum, cecum, and colon samples as detected by selective cultivation. No significant changes in the rat fecal microbiota were observed after dosage with nisin. Pearson cluster analysis of denaturing gradient gel electrophoresis profiles of the 16S rRNA genes present in the fecal microbial population revealed that the microbiota of animals dosed with either of the two L. lactis strains were different from that of control animals dosed with saline. However, profiles of the microbiota from animals dosed with nisin did not differ from the controls. The concentrations of nisin estimated by competitive enzyme-linked immunosorbent assay (ELISA) were approximately 10-fold higher in the small intestine and 200-fold higher in feces than the corresponding concentrations estimated by a biological assay. This indicates that nisin was degraded or inactivated in the gastrointestinal tract, since fragments of this bacteriocin are detected by ELISA while an intact molecule is needed to retain biological activity. 相似文献
37.
MicroRNAs (miRNAs), non-coding RNAs regulating gene expression, are frequently aberrantly expressed in human cancers. Next-generation deep sequencing technology enables genome-wide expression profiling of known miRNAs and discovery of novel miRNAs at unprecedented quantitative and qualitative accuracy. Deep sequencing was performed on 11 fresh frozen clear cell renal cell carcinoma (ccRCC) and adjacent non-tumoral renal cortex (NRC) pairs, 11 additional frozen ccRCC tissues, and 2 ccRCC cell lines (n?=?35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. those without disease recurrence, with recurrence and with metastatic disease at diagnosis. Thirty-two consecutive samples (16 ccRCC/NRC pairs) were used for stem-loop PCR validation. Novel miRNAs were predicted using 2 distinct bioinformatic pipelines. In total, 463 known miRNAs (expression frequency 1-150,000/million) were identified. We found that 100 miRNA were significantly differentially expressed between ccRCC and NRC. Differential expression of 5 miRNAs was confirmed by stem-loop PCR in the 32 ccRCC/NRC samples. With respect to RCC subgroups, 5 miRNAs discriminated between non-recurrent versus recurrent and metastatic disease, whereas 12 uniquely distinguished non-recurrent versus metastatic disease. Blocking overexpressed miR-210 or miR-27a in cell line SKCR-7 by transfecting specific antagomirs did not result in significant changes in proliferation or apoptosis. Twenty-three previously unknown miRNAs were predicted in silico. Quantitative genome-wide miRNA profiling accurately separated ccRCC from (benign) NRC. Individual differentially expressed miRNAs may potentially serve as diagnostic or prognostic markers or future therapeutic targets in ccRCC. The biological relevance of candidate novel miRNAs is unknown at present. 相似文献
38.
Hypotheses tests in bioinformatics can often be set in a tree structure in a very natural way, e.g. when tests are performed at probe, gene, and chromosome level. Exploiting this graph structure in a multiple testing procedure may result in a gain in power or increased interpretability of the results.We present the inheritance procedure, a method of familywise error control for hypotheses structured in a tree. The method starts testing at the top of the tree, following up on those branches in which it finds significant results, and following up on leaf nodes in the neighborhood of those leaves. The method is a uniform improvement over a recently proposed method by Meinshausen. The inheritance procedure has been implemented in the globaltest package which is available on www.bioconductor.org. 相似文献
39.
Monomeric red fluorescent proteins (mRFPs) have become indispensable tools for studying protein dynamics, interactions and functions in the cellular environment. Their emission spectrum can be well separated from other fluorescent proteins, and their monomeric structure preserves the natural function of fusion proteins. However, previous photophysical studies of some RFPs have shown the presence of light-induced dark states that can complicate the interpretation of cellular experiments. In this article, we extend these studies to mRFP1, mCherry, and mStrawberry by means of fluorescence correlation spectroscopy and prove that this light-driven intensity flickering also occurs in these proteins. Furthermore, we show that the flickering in these proteins is pH-dependent. Single molecule spectroscopy revealed reversible transitions from a bright to a dark state in several timescales, even up to seconds. Time-resolved fluorescence spectroscopy showed multiexponential decays, consistent with a “loose” conformation. We offer a structural basis for the fluorescence flickering using known crystal structures and point out that the environment of Glu-215 is critical for the pH dependence of the flickering in RFPs. We apply dual-color fluorescence correlation spectroscopy inside live cells to prove that this flickering can seriously hamper cellular measurements if the timescales of the flickering and diffusion are not well separated. 相似文献
40.
Transformation of Leuconostoc carnosum 4010 and Evidence for Natural Competence of the Organism 下载免费PDF全文
Sren Helmark Mette E. Hansen Birthe Jelle Kim I. Srensen Peter R. Jensen 《Applied microbiology》2004,70(6):3695-3699
Plasmid transformation in Leuconostoc carnosum 4010 was analyzed. A successful transformation protocol for L. carnosum was established by modifying an existing protocol for Lactococcus lactis. Several parameters, including the number of generations that the cells had grown at the time of harvest, glycine concentration, the time of incubation for phenotypic expression, and the electrical field strength, were investigated and proved to have influence on the transformation frequency. Electrocompetence was found to be transient and to peak in the early exponential growth phase. Optimized conditions resulted in transformation frequencies of up to 6.7 × 105 transformants per microgram of plasmid DNA. A total of five plasmids in L. carnosum were successfully introduced and maintained. Interestingly, we discovered that DNA uptake was of a frequency of 3 × 10−6 to 19 × 10−6 transformants per CFU in the absence of an applied electrical field. We concluded that L. carnosum is naturally competent. 相似文献