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Search Results: 1 - 10 of 463557 matches for " Ljiljana Pa?a-Toli? "
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FRET Imaging of Diatoms Expressing a Biosilica-Localized Ribose Sensor
Kathryn E. Marshall, Errol W. Robinson, Shawna M. Hengel, Ljiljana Paa-Toli, Guritno Roesijadi
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033771
Abstract: Future materials are envisioned to include bio-assembled, hybrid, three-dimensional nanosystems that incorporate functional proteins. Diatoms are amenable to genetic modification for localization of recombinant proteins in the biosilica cell wall. However, the full range of protein functionalities that can be accommodated by the modified porous biosilica has yet to be described. Our objective was to functionalize diatom biosilica with a reagent-less sensor dependent on ligand-binding and conformational change to drive FRET-based signaling capabilities. A fusion protein designed to confer such properties included a bacterial periplasmic ribose binding protein (R) flanked by CyPet (C) and YPet (Y), cyan and yellow fluorescent proteins that act as a FRET pair. The structure and function of the CRY recombinant chimeric protein was confirmed by expression in E. coli prior to transformation of the diatom Thalassiosira pseudonana. Mass spectrometry of the recombinant CRY showed 97% identity with the deduced amino acid sequence. CRY with and without an N-terminal Sil3 tag for biosilica localization exhibited characteristic ribose-dependent changes in FRET, with similar dissociation constants of 123.3 μM and 142.8 μM, respectively. The addition of the Sil3 tag did not alter the affinity of CRY for the ribose substrate. Subsequent transformation of T. pseudonana with a vector encoding Sil3-CRY resulted in fluorescence localization in the biosilica and changes in FRET in both living cells and isolated frustules in response to ribose. This work demonstrated that the nano-architecture of the genetically modified biosilica cell wall was able to support the functionality of the relatively complex Sil3-CyPet-RBP-YPet fusion protein with its requirement for ligand-binding and conformational change for FRET-signal generation.
Enhanced top-down characterization of histone post-translational modifications
Zhixin Tian, Nikola Toli, Rui Zhao, Ronald J Moore, Shawna M Hengel, Errol W Robinson, David L Stenoien, Si Wu, Richard D Smith, Ljiljana Paa-Toli
Genome Biology , 2012, DOI: 10.1186/gb-2012-13-10-r86
Abstract: Histones are important chromatin proteins that act as spools to package and order DNA into structural and manageable chromosomes. Core histones are modified by multiple post-translational modifications (PTMs) such as lysine acetylation, lysine or arginine methylation, and serine or threonine phosphorylation, among others. These PTMs generate a 'histone code' [1] that is implicated in chromatin-related cellular processes [2] including transcription [3], replication [4], repair [5], and alternative splicing [6].Although core histones comprise only four families (H4, H2B, H2A, and H3), each family has thousands of potential isoforms generated by different combinations of PTMs and protein sequence variation. Traditional antibody-based methods target specific isoforms, typically analyzing one PTM at a time, which makes it virtually impossible to measure combinatorial modifications occurring within the same histone molecule. Recently, high-throughput bottom-up [7] and middle-down [8] proteomic methods demonstrated potential for global characterization of PTMs on histone tails. However, these methods are ill-suited for characterizing multiple PTMs dispersed along the entire protein sequence that have been previously discovered to have significant participation in chromatin regulation [2,9-11].Top-down proteomic and high-throughput approaches are clearly required to identify and quantify the modulation of multiple intra-molecular histone modifications that synergistically regulate histone functions. Recently, a global top-down study demonstrated the feasibility of intact protein analysis for this purpose by identifying more than 300 histone isoforms using extensive fractionation and customized bioinformatics for global proteome characterization [12]. In histone-focused studies, top-down approaches using an offline two-dimensional liquid chromatography (2D LC) separation and Fourier transform mass spectrometry (FTMS) characterized 34 H4 isoforms from approximately 150 μg of
Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams
John Daniel DeBord, Donald F. Smith, Christopher R. Anderton, Ron M. A. Heeren, Ljiljana Paa-Toli, Richard H. Gomer, Francisco A. Fernandez-Lima
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0099319
Abstract: High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral resolution are needed to enable this. In this report, we employed Bi3 bombardment time-of-flight (Bi3 ToF-SIMS) and C60 bombardment Fourier transform ion cyclotron resonance secondary ion mass spectrometry (C60 FTICR-SIMS) to image Dictyostelium discoideum aggregation streams. Nearly 300 lipid species were identified from the aggregation streams. High resolution mass spectrometry imaging (FTICR-SIMS) enabled the generation of multiple molecular ion maps at the nominal mass level and provided good coverage for fatty acyls, prenol lipids, and sterol lipids. The comparison of Bi3 ToF-SIMS and C60 FTICR-SIMS suggested that while the first provides fast, high spatial resolution molecular ion images, the chemical complexity of biological samples warrants the use of high resolution analyzers for accurate ion identification.
High Mass Accuracy and High Mass Resolving Power FT-ICR Secondary Ion Mass Spectrometry for Biological Tissue Imaging
Donald F. Smith,Andras Kiss,Franklin E. Leach III,Errol W. Robinson,Ljiljana Paa-Toli,Ron M. A. Heeren
Physics , 2013, DOI: 10.1007/s00216-013-7048-1
Abstract: Biological tissue imaging by secondary ion mass spectrometry has seen rapid development with the commercial availability of polyatomic primary ion sources. Endogenous lipids and other small bio-molecules can now be routinely mapped on the sub-micrometer scale. Such experiments are typically performed on time-of-flight mass spectrometers for high sensitivity and high repetition rate imaging. However, such mass analyzers lack the mass resolving power to ensure separation of isobaric ions and the mass accuracy for elemental formula assignment based on exact mass measurement. We have recently reported a secondary ion mass spectrometer with the combination of a C60 primary ion gun with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for high mass resolving power, high mass measurement accuracy and tandem mass spectrometry capabilities. In this work, high specificity and high sensitivity secondary ion FT-ICR MS was applied to chemical imaging of biological tissue. An entire rat brain tissue was measured with 150 um spatial resolution (75 um primary ion spot size) with mass resolving power (m/{\Delta}m50%) of 67,500 (at m/z 750) and root-mean-square measurement accuracy less than two parts-per-million for intact phospholipids, small molecules and fragments. For the first time, ultra-high mass resolving power SIMS has been demonstrated, with m/{\Delta}m50% > 3,000,000. Higher spatial resolution capabilities of the platform were tested at a spatial resolution of 20 um. The results represent order of magnitude improvements in mass resolving power and mass measurement accuracy for SIMS imaging and the promise of the platform for ultra-high mass resolving power and high spatial resolution imaging.
Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans
Si Wu,Roslyn N. Brown,Samuel H. Payne,Da Meng,Rui Zhao,Nikola Toli,Li Cao,Anil Shukla,Matthew E. Monroe,Ronald J. Moore,Mary S. Lipton,Ljiljana Paa-Toli
International Journal of Proteomics , 2013, DOI: 10.1155/2013/279590
Abstract: The periplasm of Gram-negative bacteria is a dynamic and physiologically important subcellular compartment where the constant exposure to potential environmental insults amplifies the need for proper protein folding and modifications. Top-down proteomics analysis of the periplasmic fraction at the intact protein level provides unrestricted characterization and annotation of the periplasmic proteome, including the post-translational modifications (PTMs) on these proteins. Here, we used single-dimension ultra-high pressure liquid chromatography coupled with the Fourier transform mass spectrometry (FTMS) to investigate the intact periplasmic proteome of Novosphingobium aromaticivorans. Our top-down analysis provided the confident identification of 55 proteins in the periplasm and characterized their PTMs including signal peptide removal, N-terminal methionine excision, acetylation, glutathionylation, pyroglutamate, and disulfide bond formation. This study provides the first experimental evidence for the expression and periplasmic localization of many hypothetical and uncharacterized proteins and the first unrestrictive, large-scale data on PTMs in the bacterial periplasm. 1. Introduction The periplasm of Gram-negative bacteria is a hydrated gel located between the cytoplasmic and outer membranes and is comprised of peptidoglycan (cell wall), proteins, carbohydrates, and small solutes [1–3]. The periplasm is a dynamic subcellular compartment important for trafficking of molecules into and out of cells, maintaining cellular osmotic balance, envelope structure, responding to environmental cues and stresses, electron transport, xenobiotic metabolism, and protein folding and modification [4]. The periplasm provides a good model system to study protein biogenesis, composition, sorting, and modification at the molecular level. Indeed, it is analogous in many ways to the endoplasmic reticulum of eukaryotic cells in terms of transport, folding, and quality control [3]. Localization to the periplasm and beyond often involves an N-terminal secretion signal that targets the protein for translocation across the cytoplasmic membrane via the general secretory pathway [5]. These secretion signals (also known as signal peptides) are cleaved by signal peptidases located in the cytoplasmic membrane [6]. Thus, it is expected that signal peptide cleavage is a common modification in the periplasmic proteome. Compared to the cytoplasm, the periplasm is more vulnerable to changes in pH, temperature, and osmolarity in the external environment [4, 7, 8]. For structural stability in
Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
Patrik D'haeseleer, John M. Gladden, Martin Allgaier, Patrik S. G. Chain, Susannah G. Tringe, Stephanie A. Malfatti, Joshua T. Aldrich, Carrie D. Nicora, Errol W. Robinson, Ljiljana Paa-Toli, Philip Hugenholtz, Blake A. Simmons, Steven W. Singer
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0068465
Abstract: Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.
Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer
Diederick Duijvesz, Kristin E. Burnum-Johnson, Marina A. Gritsenko, A. Marije Hoogland, Mirella S. Vredenbregt-van den Berg, Rob Willemsen, Theo Luider, Ljiljana Paa-Toli, Guido Jenster
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0082589
Abstract: Background Current markers for prostate cancer, such as PSA lack specificity. Therefore, novel biomarkers are needed. Unfortunately, the complexity of body fluids often hampers biomarker discovery. An attractive alternative approach is the isolation of small vesicles, i.e. exosomes, ~100 nm, which contain proteins that are specific to the tissue from which they are derived and therefore can be considered as treasure chests for disease-specific biomarker discovery. Materials and Methods Exosomes were isolated from 2 immortalized primary prostate epithelial cells (PNT2C2 and RWPE-1) and 2 PCa cell lines (PC346C and VCaP) by ultracentrifugation. After tryptic digestion, proteomic analyses utilized a nanoLC coupled with an LTQ-Orbitrap operated in tandem MS (MS/MS) mode. Accurate Mass and Time (AMT) tag approach was employed for peptide identification and quantitation. Candidate biomarkers were validated by Western blotting and Immunohistochemistry. Results Proteomic characterization resulted in the identification of 248, 233, 169, and 216 proteins by at least 2 peptides in exosomes from PNT2C2, RWPE-1, PC346C, and VCaP, respectively. Statistical analyses revealed 52 proteins differently abundant between PCa and control cells, 9 of which were more abundant in PCa. Validation by Western blotting confirmed a higher abundance of FASN, XPO1 and PDCD6IP (ALIX) in PCa exosomes. Conclusions Identification of exosomal proteins using high performance LC-FTMS resulted in the discovery of PDCD6IP, FASN, XPO1 and ENO1 as new candidate biomarkers for prostate cancer.
Solid insulation drying of 110 kV paper-oil instrument transformers
Gerards Gavrilovs , Sandra Vītoli a
Scientific Journal of Riga Technical University. Power and Electrical Engineering , 2009, DOI: 10.2478/v10144-009-0007-1
Abstract: Influence of moisture on the instrument transformers' paper-oil insulation and its further maintenance is described in this paper. Improved insulation drying method using vacuum and temperature regulation with definite regulation algorithm of parameters is proposed and analyzed by comparing it with conventional drying method.
The influence of non-ideal phase flow on the extraction efficiency for the case of a linear equilibrium distribution
Tadi? G.,Gligori? M.,ToliA.
Journal of Mining and Metallurgy, Section B : Metallurgy , 2006, DOI: 10.2298/jmmb0601067t
Abstract: The influence of the fundamental parameters of non-ideal phase flow and the extraction parameters on the number of equilibrium stages - ND, theoretical stages - NT, as well as the number of stages (ND - NT), the existence of which is a consequence of the backflow in extractors, was investigated. The calculated number of stages (ND - NT) served as a measure of the influence of the denoted parameters on the extraction efficiency. The results of the investigation indicate that the number of stages (ND - NT) considerably increased with increasing backmixing coefficients and that the dependence was linear. It was established that the increase of the ratio of the flow rate of the heavy and light phase and the decrease of the equilibrium distribution coefficient, as well as the increase of the total separation factor, led to an exponential increase of the number of stages in the extractor, which consequently caused a decrease in the extraction efficiency.
X and γ-rays emission probabilities of 131I and 133Xe  [PDF]
Paa Yal??n, Arif Ba?tu?
Natural Science (NS) , 2011, DOI: 10.4236/ns.2011.37084
Abstract: Radioactive nuclides as 131I and 133Xe are increasingly used for both clinical diagnosis and therapeutic treatment of the patient. For example, 131I is used for the treatment of thyroid gland cancer. Otherwise, 133Xe is used in ventilation studies to assess and evaluate pulmonary function and to provide images of the lungs in both cardiac and pulmonary diseases, such as asthma, pulmonary emphysema, bronchiectasis, carcinoma of the lung, and pulmonary embolism [1,2]. Furthermore, cerebral blood flow is measured using 133Xe inhalation. In this study, the X and γ-rays emission probabilities in the decay of 131I and 133Xe were precisely measured with a calibrated Si(Li) detector. Results of this study were compared using available results in the literature. Good agreement was observed between our results and available results in the literature.
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