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Berlin Brandenburg

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  • 1
    In: Molecular Microbiology, December 2011, Vol.82(6), pp.1545-1562
    Description: A major class of small bacterial RNAs (sRNAs) regulate translation and mRNA stability by pairing with target mRNAs, dependent upon the RNA chaperone Hfq. Hfq, related to the Lsm/Sm families of splicing proteins, binds the sRNAs and stabilizes them and stimulates pairing with mRNAs . Although Hfq is abundant, the sRNAs, when induced, are similarly abundant. Therefore, Hfq may be limiting for sRNA function. We find that, when overexpressed, a number of sRNAs competed with endogenous sRNAs for binding to Hfq. This correlated with lower accumulation of the sRNAs (presumably a reflection of the loss of Hfq binding), and lower activity of the sRNAs in regulating gene expression. Hfq was limiting for both positive and negative regulation by the sRNAs. In addition, deletion of the gene for an expressed and particularly effective competitor sRNA improved the regulation of genes by other sRNAs, suggesting that Hfq is limiting during normal growth conditions. These results support the existence of a hierarchy of sRNA competition for Hfq, modulating the function of some sRNAs.
    Keywords: Messenger Rna ; Protein Binding ; Gene Expression ; Genes ; Escherichia Coli ; Proteins;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 2
    Language: English
    In: Biochemical and Biophysical Research Communications, 17 February 2012, Vol.418(3), pp.475-482
    Description: ► ChIP-Seq analysis of histone modifications in breast cancer and normal cells. ► Identification of differentially modified chromatin regions as regulatory elements. ► Assessment of transcriptional activity for cell-type specific enhancers. Histone modifications are regarded as one of markers to identify regulatory elements which are DNA segments modulating gene transcription. Aberrant changes of histone modification levels are frequently observed in cancer. We have employed ChIP-Seq to identify regulatory elements in human breast cancer cell line, MCF-7 by comparing histone modification patterns of H3K4me1, H3K4me3, and H3K9/14ac to those in normal mammary epithelial cell line, MCF-10A. The genome-wide analysis shows that H3K4me3 and H3K9/14ac are highly enriched at promoter regions and H3K4me1 has a relatively broad distribution over proximity of TSSs as well as other genomic regions. We identified that many differentially expressed genes in MCF-7 have divergent histone modification patterns. To understand the functional roles of distinctively histone-modified regions, we selected 35 genomic regions marked by at least one histone modification and located from 3 to 10 kb upstream of TSS in both MCF-7 and MCF-10A and assessed their transcriptional activities. About 66% and 60% of selected regions in MCF-7 and MCF-10A, respectively, enhanced the transcriptional activity. Interestingly, most regions marked by H3K4me1 exhibited an enhancer activity. Regions with two or more kinds of histone modifications did show varying activities. In conclusion, our data reflects that comprehensive analysis of histone modification profiles under cell type-specific chromatin environment should provide a better chance for defining functional regulatory elements in the genome.
    Keywords: Breast Cancer ; Histone Modification ; Epigenome ; Regulatory Elements ; Enhancer ; Biology ; Chemistry ; Anatomy & Physiology
    ISSN: 0006-291X
    E-ISSN: 1090-2104
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  • 3
    Language: English
    In: Proceedings Of The 55th Annual Conference On Magnetism And Magnetic Materials, Atlanta, Georgia (14-18 November 2010):
    In: Journal of Applied Physics, 01 April 2012, Vol.111(7)
    Description: Using micromagnetic simulation, we investigate the effect of enhanced damping induced by spin-motive force on the vortex dynamics. It is found that the enhanced damping does not affect the resonance frequency of gyrotropic motion. However, it changes the gyration radius, the velocity of a vortex core, and the dynamics of core reversal. During the gyrotropic motion, the additional damping goes up to three times larger than a typical value of the intrinsic damping. Moreover, in the case of core reversal, the additional damping becomes 10 times larger than the intrinsic damping. For vortex dynamics, the enhanced damping due to spin-motive is non-negligible and thus should be considered to understand experimental results.
    Keywords: Proceedings Of The 56th Annual Conference On Magnetism And Magnetic Materials
    ISSN: 0021-8979
    E-ISSN: 1089-7550
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  • 4
    In: Molecular Microbiology, July 2013, Vol.89(1), pp.52-64
    Description: The / two‐component system activates many genes for lipopolysaccharide () modification when cells are grown at low concentrations. An additional target of and is , an Hfq‐dependent small that negatively regulates expression of , also encoding a protein that carries out modification. Examination of confirmed that effectively silences ; the phosphoethanolamine modification associated with is found in Δ::kan but not cells. igma has been reported to positively regulate , although the promoter does not have the expected igma recognition motifs. The effects of igma and deletion of on levels of were independent, and the same 5′ end was found in both cases. transcription and the behaviour of transcriptional and translational fusions demonstrate that igma acts directly at the level of transcription initiation for , from the same start point as igma 70. The results suggest that when igma is active, synthesis of transcript outstrips ‐dependent degradation; presumably the modification of is important under these conditions. Adding to the complexity of regulation is a second , , which also directly and negatively regulates .
    Keywords: Transcription (Genetics) -- Genetic Aspects ; Enzymes -- Genetic Aspects ; Rna -- Genetic Aspects ; Mitogens;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 10 February 2015, Vol.112(6), pp.E526-35
    Description: Two-component systems [sensor kinase/response regulator (RR)] are major tools used by microorganisms to adapt to environmental conditions. RR phosphorylation is typically required for gene activation, but few studies have addressed how and if phosphorylation affects specific steps during transcription initiation. We characterized transcription complexes made with RNA polymerase and the Bordetella pertussis RR, BvgA, in its nonphosphorylated or phosphorylated (BvgA∼P) state at P(fim3), the promoter for the virulence gene fim3 (fimbrial subunit), using gel retardation, potassium permanganate and DNase I footprinting, cleavage reactions with protein conjugated with iron bromoacetamidobenzyl-EDTA, and in vitro transcription. Previous work has shown that the level of nonphosphorylated BvgA remains high in vivo under conditions in which BvgA is phosphorylated. Our results here indicate that surprisingly both BvgA and BvgA∼P form open and initiating complexes with RNA polymerase at P(fim3). However, phosphorylation of BvgA is needed to generate the correct conformation that can transition to competent elongation. Footprints obtained with the complexes made with nonphosphorylated BvgA are atypical; while the initiating complex with BvgA synthesizes short RNA, it does not generate full-length transcripts. Extended incubation of the BvgA/RNA polymerase initiated complex in the presence of heparin generates a stable, but defective species that depends on the initial transcribed sequence of fim3. We suggest that the presence of nonphosphorylated BvgA down-regulates P(fim3) activity when phosphorylated BvgA is present and may allow the bacterium to quickly adapt to the loss of inducing conditions by rapidly eliminating P(fim3) activation once the signal for BvgA phosphorylation is removed.
    Keywords: Bordetella Pertussis ; Bvga ; RNA Polymerase ; Fim3 ; Transcription ; Adaptation, Physiological -- Physiology ; Antigens, Bacterial -- Metabolism ; Bacterial Proteins -- Metabolism ; Bordetella Pertussis -- Genetics ; Fimbriae Proteins -- Metabolism ; Gene Expression Regulation, Bacterial -- Physiology ; Multiprotein Complexes -- Metabolism ; Transcription Factors -- Metabolism ; Transcription, Genetic -- Physiology ; Virulence Factors, Bordetella -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    Language: English
    In: Tetrahedron Letters, 2010, Vol.51(25), pp.3290-3293
    Description: A novel feric ion-selective rhodamine-based fluorescent chemosensor, which contains a bis-aminoxy chain moiety, has been developed. The multi-dentate binding site of rhodamine fluorophore shows selective detection of ferric iron over other biologically important metal ions in aqueous media and also shows 1:1 binding stoichiometry.
    Keywords: Chemistry
    ISSN: 0040-4039
    E-ISSN: 1873-3581
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  • 7
    Language: English
    In: The Journal of Urology, 2011, Vol.186(2), pp.423-429
    Description: Cystic renal cell carcinoma has more favorable biology than noncystic renal cell carcinoma. Recently cystic change detected grossly or by low power microscopy was found to be a good prognostic factor for clear cell renal cell carcinoma. We assessed the optimal cutoff value of the proportion of cystic change with prognostic significance for clear cell renal cell carcinoma. We identified 223 patients with clear cell renal cell carcinoma who underwent partial or radical nephrectomy between 2001 and 2003. The cystic proportion of the tumor cut surface was calculated objectively and its prognostic significance was evaluated. The ROC curve showed that a cystic percent of between 6% and 10% was appropriate to detect patients with renal cell carcinoma at low risk for cancer mortality and progression. A cutoff of 6% was adopted as a break point of cystic change for patient stratification. We analyzed the records of 87 patients (39.0%) with tumors with a cystic proportion of greater than 5%, that is 6% or greater. They had significantly lower stage and lower Fuhrman nuclear grade than patients with tumors with a cystic change of 5% or less (each p 〈0.0001). On multivariate analysis a cystic proportion of more than 5% was a good prognostic indicator of cancer specific and progression-free survival (HR 0.221, p = 0.044 and HR 0.214, p = 0.004, respectively). In patients with clear cell renal cell carcinoma a cystic change comprising more than 5% of the tumor is a good independent predictor of survival.
    Keywords: Kidney ; Carcinoma ; Renal Cell ; Cysts ; Mortality ; Republic of Korea ; Medicine
    ISSN: 0022-5347
    E-ISSN: 1527-3792
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  • 8
    Language: English
    In: Clinical Neurophysiology, 2011, Vol.122(11), pp.2310-2311
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.clinph.2011.04.015 Byline: Jeeyoung Oh (a), Moon-Kyung Sunwoo (b), Il Nam Sunwoo (b) Author Affiliation: (a) Department of Neurology, Konkuk University School of Medicine, Seoul, Republic of Korea (b) Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea Article History: Accepted 13 April 2011
    Keywords: Medicine
    ISSN: 1388-2457
    E-ISSN: 1872-8952
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  • 9
    Language: English
    In: Science of the Total Environment, 01 April 2013, Vol.449, pp.95-101
    Description: Photo-decomposition of methylmercury (MeHg) in surface water is thought to be an important process that reduces the bioavailability of mercury (Hg) to aquatic organisms. In this study, photo-initiated decomposition of MeHg was investigated under UVA irradiation in the presence of natural water constituents including NO , Fe , and HCO ions, and dissolved organic matter such as humic and fulvic acid. MeHg degradation followed the pseudo-first-order kinetics; the rate constant increased with increasing UVA intensity (0.3 to 3.0 mW cm ). In the presence of NO , Fe , and fulvic acid, the decomposition rate of MeHg increased significantly due to photosensitization by reactive species such as hydroxyl radical. The presence of humic acid and HCO ions lowered the degradation rate through a radical scavenging effect. Increasing the pH of the solution increased the degradation rate constant by enhancing the generation of hydroxyl radicals. Hydroxyl radicals play an important role in the photo-decomposition of MeHg in water, and natural constituents in water can affect the photo-decomposition of MeHg by changing radical production and inhibition. ► The abiotic photodecomposition of methylmercury (MeHg) in water was examined. ► UVA light is a primary factor inducing MeHg photodecomposition in water. ► Fulvic acid, NO , and Fe ion increased MeHg photo-decomposition rate significantly. ► Humic acid and HCO ions inhibited photodecomposition through radical scavenging. ► OH radical is an important compound affecting photodecomposition of MeHg in water.
    Keywords: Fulvic Acid ; Humic Acid ; Nitrate ; Bicarbonate ; Demethylation ; Hydroxyl Radical ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 10
    Language: English
    In: Science of the total environment, 2013, Vol.449, pp.95-101
    Description: Photo-decomposition of methylmercury (MeHg) in surface water is thought to be an important process that reduces the bioavailability of mercury (Hg) to aquatic organisms. In this study, photo-initiated decomposition of MeHg was investigated under UVA irradiation in the presence of natural water constituents including NO₃ ⁻, Fe³⁺, and HCO₃ ⁻ ions, and dissolved organic matter such as humic and fulvic acid. MeHg degradation followed the pseudo-first-order kinetics; the rate constant increased with increasing UVA intensity (0.3 to 3.0mWcm⁻²). In the presence of NO₃ ⁻, Fe³⁺, and fulvic acid, the decomposition rate of MeHg increased significantly due to photosensitization by reactive species such as hydroxyl radical. The presence of humic acid and HCO₃ ⁻ ions lowered the degradation rate through a radical scavenging effect. Increasing the pH of the solution increased the degradation rate constant by enhancing the generation of hydroxyl radicals. Hydroxyl radicals play an important role in the photo-decomposition of MeHg in water, and natural constituents in water can affect the photo-decomposition of MeHg by changing radical production and inhibition. ; p. 95-101.
    Keywords: Hydroxyl Radicals ; Aquatic Organisms ; Irradiation ; Surface Water ; Bioavailability ; Fulvic Acids ; Humic Acids ; Ions ; Methylmercury Compounds ; Ph ; Mercury
    ISSN: 0048-9697
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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