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Search Results: 1 - 10 of 655 matches for " Nikola Toli? "
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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 Pa?a-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
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 Pa?a-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
Symbolic Form in the Pedagogical Implications of Sociolinguistics
Mirela Toli
World Journal of Education , 2011, DOI: 10.5430/wje.v1n1p158
Abstract: The author with the help of analysis of symbolic forms and sociolinguistics explains the transformation of homo communicans in conscious homo symbolicum. He points out the importance of etymological analysis Cassierer's philosophy of symbolic forms and its effects in the modern understanding of sociolinguistics. It is necessary their correlation relationship for the development of critical-reflective attitude towards the accelerated development of new media...The article provides an overview of pedagogical implications in the analysis of symbols and sociolinguistics in the educational process. Sociolinguistics is analyzed in terms of its impact on the development of media pedagogy in Croatia.
Hidden Polynomial(s) Cryptosystems
Ilia Toli
Computer Science , 2003,
Abstract: We propose variations of the class of hidden monomial cryptosystems in order to make it resistant to all known attacks. We use identities built upon a single bivariate polynomial equation with coefficients in a finite field. Indeed, it can be replaced by a ``small'' ideal, as well. Throughout, we set up probabilistic encryption protocols, too. The same ideas extend to digital signature algorithms, as well. Our schemes work as well on differential fields of positive characteristic, and elsewhere.
Singularity of Sparse Circulant Matrices is NP-complete
Ilia Toli
Computer Science , 2009,
Abstract: It is shown by Karp reduction that deciding the singularity of $(2^n - 1) \times (2^n - 1)$ sparse circulant matrices (SC problem) is NP-complete. We can write them only implicitly, by indicating values of the $2 + n(n + 1)/2$ eventually nonzero entries of the first row and can make all matrix operations with them. The positions are $0, 1, 2^{i} + 2^{j}$. The complexity parameter is $n$. Mulmuley's work on the rank of matrices \cite{Mulmuley87} makes SC stand alone in a list of 3,000 and growing NP-complete problems.
Cryptanalysis of HFE
Ilia Toli
Computer Science , 2003,
Abstract: I transform the trapdoor problem of HFE into a linear algebra problem.
Hidden Polynomial(s) Cryptosystems
Ilia Toli
Computer Science , 2003,
Abstract: We propose public-key cryptosystems with public key a system of polynomial equations, algebraic or differential, and private key a single polynomial or a small-size ideal. We set up probabilistic encryption, signature, and signcryption protocols.
Blood Peptidome-Degradome Profile of Breast Cancer
Yufeng Shen,Nikola Toli,Tao Liu,Rui Zhao,Brianne O. Petritis,Marina A. Gritsenko,David G. Camp,Ronald J. Moore,Samuel O. Purvine,Francisco J. Esteva,Richard D. Smith
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013133
Abstract: Cancer invasion and metastasis are closely associated with activities within the degradome; however, little is known about whether these activities can be detected in the blood of cancer patients.
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium
Charles Ansong, Nikola Toli, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith, Scott N Peterson, Fred Heffron, Michael McClelland, Joshua N Adkins
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-433
Abstract: We experimentally annotated the bacterial pathogen Salmonella Typhimurium 14028, using "shotgun" proteomics to accurately uncover the translational landscape and post-translational features. The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in Salmonella and suggest revisions to several genes that appear to have incorrectly assigned translational start sites, including a potential novel alternate start codon. Additionally, we uncovered 12 non-annotated genes missed by gene prediction programs, as well as evidence suggesting a role for one of these novel ORFs in Salmonella pathogenesis. We also characterized post-translational features in the Salmonella genome, including chemical modifications and proteolytic cleavages. We find that bacteria have a much larger and more complex repertoire of chemical modifications than previously thought including several novel modifications. Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function.This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive proteome map of Salmonella as a resource for systems analysis.Many aspects of modern biological research are dependent on accurate identification of the protein-coding genes in each genome, as well as the nature of the mature functional protein products, a process commonly referred to as genome annotation. With the exponential increase in the number of sequenced prokaryotic genomes afforded by advances in genome sequencing technologies over the last decade, present day prokaryotic genome annotation is essentially an automated high-throughput process that relies heavily on de novo gene prediction programs [1-3].While de novo gene prediction programs have significantly improved for prokaryotic genomes consider
The Effectiveness of the Functional Magnetic Stimulation Therapy in Treating Sciatica Syndrome  [PDF]
Tamara Radakovi?, Nikola Radakovi?
Open Journal of Therapy and Rehabilitation (OJTR) , 2015, DOI: 10.4236/ojtr.2015.33009
Abstract: Introduction: Degenerative or traumatic causes are most common in generating sciatica syndrome, which is normally treated with well-known physical therapy methods. A relatively new way of treating sciatica problems is so-called functional magnetic stimulation (FMS), whose principle is based on electromagnetic field inducing electrical field inside the body. Electrical field triggers action potential of nerve cells and that way stimulates peripheral motor nerve system. Aim: Aim of this study is to measure and estimate the effectiveness of implementing therapy with functional magnetic stimulation in regular physical treatment of sciatica syndrome. Materials and Methods: 28 male patients aged between 30 and 55 with back problem were recruited on an outpatient basis. FMS therapy was performed with TESLA Stym? device (Iskra Medical d.o.o., Slovenia) treating lumbosacral region equally on both sides of the spine. Physical examination was performed to evaluate tree parameters: the mobility of the lumbar spine in flexion and extension, together with the straight leg raise test (Lasegue sign). We estimated patients’ progress, comparing angle values of mobility from the first examination day with other examination days. Results: In FMS treated group of patients, lumbosacral flexion, extension and Lasegue test angle were significantly higher compared to day 0 on the first physical examination day (day 3) (p < 0.05). In control group such increase of a measured angle was not noticed until a second physical examination day (day 5) or a third physical examination day (day 8) (p < 0.05). Discussion: Results in this study showed that applying FMS therapy along with other standard physical therapy methods rapidly increased effectiveness of the treatment of sciatica syndrome (lat. ischialgia). It suggests that functional magnetic therapy could be suggested as a regular physical therapy method in treating this kind of pain syndromes.
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