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Ubiquitous Presence (ubiquitous + presence)
Selected AbstractsThe mitochondrial proteome: A dynamic functional program in tissues and disease states,ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 5 2010Robert S. Balaban Abstract The nuclear DNA transcriptional programming of the mitochondria proteome varies dramatically between tissues depending on its functional requirements. This programming generally regulates all of the proteins associated with a metabolic or biosynthetic pathway associated with a given function, essentially regulating the maximum rate of the pathway while keeping the enzymes at the same molar ratio. This may permit the same regulatory mechanisms to function at low- and high-flux capacity situations. This alteration in total protein content results in rather dramatic changes in the mitochondria proteome between tissues. A tissues mitochondria proteome also changes with disease state, in Type 1 diabetes the liver mitochondrial proteome shifts to support ATP production, urea synthesis, and fatty acid oxidation. Acute flux regulation is modulated by numerous posttranslational events that also are highly variable between tissues. The most studied posttranslational modification is protein phosphorylation, which is found all of the complexes of oxidative phosphorylation and most of the major metabolic pathways. The functional significance of these modifications is currently a major area of research along with the kinase and phosphatase regulatory network. This near ubiquitous presence of protein phosphorylations, and other posttranslational events, in the matrix suggest that not all posttranslational events have functional significance. Screening methods are being introduced to detect the active or dynamic posttranslational sites to focus attention on sites that might provide insight into regulatory mechanisms. Environ. Mol. Mutagen., 2010. Published 2010 Wiley-Liss, Inc. [source] Soluble protein oligomers as emerging toxins in alzheimer's and other amyloid diseasesIUBMB LIFE, Issue 4-5 2007Sergio T. Ferreira Abstract Amyloid diseases are a group of degenerative disorders characterized by cell/tissue damage caused by toxic protein aggregates. Abnormal production, processing and/or clearance of misfolded proteins or peptides may lead to their accumulation and to the formation of amyloid aggregates. Early histopathological investigation of affected organs in different amyloid diseases revealed the ubiquitous presence of fibrillar protein aggregates forming large deposits known as amyloid plaques. Further in vitro biochemical and cell biology studies, as well as studies using transgenic animal models, provided strong support to what initially seemed to be a solid concept, namely that amyloid fibrils played crucial roles in amyloid pathogenesis. However, recent studies describing tissue-specific accumulation of soluble protein oligomers and their strong impact on cell function have challenged the fibril hypothesis and led to the emergence of a new view: Fibrils are not the only toxins derived from amyloidogenic proteins and, quite possibly, not the most important ones with respect to disease etiology. Here, we review some of the recent findings and concepts in this rapidly developing field, with emphasis on the involvement of soluble oligomers of the amyloid-, peptide in the pathogenesis of Alzheimer's disease. Recent studies suggesting that soluble oligomers from different proteins may share common mechanisms of cytotoxicity are also discussed. Increased understanding of the cellular toxic mechanisms triggered by protein oligomers may lead to the development of rational, effective treatments for amyloid disorders. IUBMB Life, 59: 332-345, 2007 [source] Functional enhancement of Sake yeast strains to minimize the production of ethyl carbamate in Sake wineJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2010M.S. Dahabieh Abstract Aims:, In fermented alcoholic beverages and particularly in Japanese Sake wine, the ubiquitous presence of the probable human carcinogen ethyl carbamate (EC) is a topic of significant concern. This study aims to develop novel methods for the reduction of EC in Sake wine. Methods and Results:, To reduce the high levels of EC in Sake wine, urea-degrading and urea-importing yeast strains were created by integrating linear cassettes containing either the respective DUR1,2 or DUR3 genes, under the control of the constitutively active Saccharomyces cerevisiae PGK1 promoter, into the Sake yeast strains K7 and K9. The self-cloned, urea-degrading Sake strains K7DUR1,2 and K9DUR1,2 produced Sake wine with 87 and 68% less EC, respectively, while the urea-importing Sake yeast strain K7DUR3 reduced EC by 15%. All functionally enhanced yeast strains were shown to be substantially equivalent to their parental strains in terms of fermentation rate, ethanol production, phenotype and transcriptome. Conclusions:, Under the conditions tested, urea-degrading yeast (constitutive DUR1,2 expression) are superior to urea-importing yeast (constitutive DUR3 expression) for EC reduction in Sake wine, and constitutive co-expression of DUR1,2 and DUR3 does not yield synergistic EC reduction. Significance and Impact of the Study:, The self-cloned, substantially equivalent, urea-degrading Sake yeast strains K7DUR1,2 and K9DUR1,2, which contain the integrated DUR1,2 cassette, are capable of highly efficacious EC reduction during Sake brewing trials, are suitable for commercialization and are important tools for modern Sake makers in their efforts to reduce high EC levels in Sake wine. [source] Evidences of a role for eukaryotic translation initiation factor 5A (eIF5A) in mouse embryogenesis and cell differentiationJOURNAL OF CELLULAR PHYSIOLOGY, Issue 2 2010Lucas T. Parreiras-e-Silva Eukaryotic translation initiation factor 5A (eIF5A) has a unique character: the presence of an unusual amino acid, hypusine, which is formed by post-translational modifications. Even before the identification of hypusination in eIF5A, the correlation between hypusine formation and protein synthesis, shifting cell proliferation rates, had already been observed. Embryogenesis is a complex process in which cellular proliferation and differentiation are intense. In spite of the fact that many studies have described possible functions for eIF5A, its precise role is under investigation, and to date nothing has been reported about its participation in embryonic development. In this study we show that eIF5A is expressed at all mouse embryonic post-implantation stages with increase in eIF5A mRNA and protein expression levels between embryonic days E10.5 and E13.5. Immunohistochemistry revealed the ubiquitous presence of eIF5A in embryonic tissues and organs at E13.5 day. Interestingly, stronger immunoreactivity to eIF5A was observed in the stomodeum, liver, ectoderm, heart, and eye, and the central nervous system; regions which are known to undergo active differentiation at this stage, suggesting a role of eIF5A in differentiation events. Expression analyses of MyoD, a myogenic transcription factor, revealed a significantly higher expression from day E12.5 on, both at the mRNA and the protein levels suggesting a possible correlation to eIF5A. Accordingly, we next evidenced that inhibiting eIF5A hypusination in mouse myoblast C2C12 cells impairs their differentiation into myotubes and decreases MyoD transcript levels. Those results point to a new functional role for eIF5A, relating it to embryogenesis, development, and cell differentiation. J. Cell. Physiol. 225: 500,505, 2010. © 2010 Wiley-Liss, Inc. [source] Kinetics of pronuclear development and the effects of vector type and timing of injection on the efficiency of gene transfer into rhesus macaque embryosMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 10 2008H.M. Kubisch Abstract A series of experiments was performed to determine the dynamics of pronuclear development as well as the efficiency of either adenovirus-associated (AAV) or lentivirus-derived vectors to introduce a green fluorescent protein (GFP) reporter gene into rhesus macaque (Macaca mulatta) embryos. Assessment of pronuclear development at various times after fertilization revealed that the appearance of pronuclei was determined by the presence of the first and the timing of the second polar body. The dynamics of pronuclear formation was a significant determinant of whether an oocyte reached the blastocyst stage, however, when the percentage of blastocysts were based on the number of zygotes, the timing of the appearance of polar bodies did not appear to have any effect on subsequent development. Injection of different AAV-derived vectors showed that the serotype of the vector did not affect development or the proportion of transgenic embryos. Moreover, all putative transgenic embryos proved to be expression mosaics. Injection of embryos with lentiviral vectors showed that timing of injection (before or after fertilization) had no effect on subsequent transgene expression, but that the type of reporter gene determined post-injection development and rate of transgenesis. The transfer of embryos following injection of a lentiviral vector into three recipients resulted in one pregnancy which was lost during the second trimester. Analysis of fetal tissues showed ubiquitous presence of the transgene and GFP expression in all tissues examined. These results show that lentivirus-derived vectors can efficiently transform rhesus embryos and are suitable for the generation of transgenic rhesus monkeys. Mol. Reprod. Dev. 75: 1505,1514 © 2008 Wiley-Liss, Inc. [source] Haloes around edge-on disc galaxies in the Sloan Digital Sky SurveyMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2004Stefano Zibetti ABSTRACT We present a statistical analysis of halo emission for a sample of 1047 edge-on disc galaxies imaged in five bands by the Sloan Digital Sky Survey (SDSS). Stacking the homogeneously rescaled images of the galaxies, we can measure surface brightnesses as deep as ,r, 31 mag arcsec,2. The results strongly support the almost ubiquitous presence of stellar haloes around disc galaxies, whose spatial distribution is well described by a power law ,,r,3, in a moderately flattened spheroid (c/a, 0.6). The colour estimates in g,r and r,i, although uncertain, give a clear indication for extremely red stellar populations, hinting at old ages and/or non-negligible metal enrichment. These results support the idea of haloes being assembled via early merging of satellite galaxies. [source] Increasing the mass accuracy of high-resolution LC-MS data using background ions , a case study on the LTQ-OrbitrapPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2008Richard A. Scheltema Abstract With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel computational method that improves the mass accuracy of the LTQ-Orbitrap mass spectrometer from an initial ±1,2,ppm, obtained by the standard software, to an absolute median of 0.21,ppm (SD 0.21,ppm). With the increased mass accuracy it becomes much easier to match mass chromatograms in replicates and different sample types, even if compounds are detected at very low intensities. The proposed method exploits the ubiquitous presence of background ions in LC-MS profiles for accurate alignment and internal mass calibration, making it applicable for all types of MS equipment. The accuracy of this approach will facilitate many downstream systems biology applications, including mass-based molecule identification, ab initio metabolic network reconstruction, and untargeted metabolomics in general. [source] Effect of yeast extract on speciation and bioavailability of nickel and cobalt in anaerobic bioreactorsBIOTECHNOLOGY & BIOENGINEERING, Issue 2 2003G. Gonzalez-Gil Abstract The speciation of metals plays an important role in their bioavailability. In the case of anaerobic reactors for the treatment of wastewaters, the ubiquitous presence of sulfide leads to extensive precipitation of metals like nickel and cobalt, which are essential for the metabolism of the anaerobic microorganisms that carry out the mineralization of the pollutants present in the wastewater. In practice, nickel, cobalt, and iron are added in excessive amounts to full-scale installations. This study is concerned with the complexation of nickel and cobalt with yeast extract and its effect on the biogas production by methanogenic biomass. Adsorptive stripping voltammetry (AdSV) was used to get information about the stability and complexing capacity of the metal,yeast extract complexes formed. Nickel and cobalt form relatively strong organic complexes with yeast extract. The bioavailability of these essential metals in anaerobic batch reactors was dramatically increased by the addition of yeast extract. This is due to the formation of dissolved bioavailable complexes, which favors the dissolution of metals from their sulfides. Trace doses of yeast extract may be effective in keeping additions of essential metals to anaerobic reactors at a minimum. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 134,142, 2003. [source] The hepatitis E virus ORF3 protein stabilizes HIF-1, and enhances HIF-1-mediated transcriptional activity through p300/CBPCELLULAR MICROBIOLOGY, Issue 9 2009Syed M. Moin Summary The hepatitis E virus (HEV) causes hepatitis E and is an important human pathogen. We have previously shown that the HEV open reading frame 3 (ORF3) protein promotes survival of the host cell. Here we report finding increased expression of glycolytic pathway enzymes in ORF3-expressing cells. Promoter analysis of these genes revealed the ubiquitous presence of hypoxia inducible factor (HIF) responsive element (HRE). Dominant-negative and siRNA studies showed increased expression of glycolytic pathway genes by the ORF3 to be mediated by the HIF-1 transcription factor. Our results showed that HIF-1,, a highly unstable subunit of the HIF-1, was stabilized in ORF3-expressing cells. This was through phosphatidylinositol-3-kinase (PI3K) mediated activation of Akt/protein kinase B. Enhanced binding to the consensus HRE and increased transactivation activity of HIF-1 were also observed in ORF3-expressing cells. The HIF complex recruits the transcriptional adapter/histone acetyltransferase protein p300/CBP to target gene promoters and p300/CBP phosphorylation is required for this interaction. We show that ORF3-mediated extracellularly regulated kinase (Erk) activation was responsible for the observed increase in phosphorylation and transactivation activity of p300/CBP. Our results reveal a two-pronged strategy through which the ORF3 protein might modulate the energy homeostasis in HEV infected cells and thus contribute to pathogenesis. [source] | ||||||||||