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Search Results: 1 - 10 of 492 matches for " Roumiana VASSILEVSKA-IVANOVA "
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Journal of Central European Agriculture , 2012, DOI: 10.5513/jcea01/13.3.1070
Abstract: A protocol for indirect shoot organogenesis of Solanum melongena ‘Larga Negra’ and ‘Black Beauty’ was established using hypocotyl and cotyledon derived calluses. The maximum morphogenic callus induction was observed from cultured cotyledons of 30-days old seedlings on Murashige and Skoog (MS) medium containing 2.0 mg/l α-naphthalene acetic acid and 0.5 mg/l 6-benzylaminopurine. The highest percentage of shoot regeneration and the highest mean number of shoots/callus were obtained on hormone-free MS medium. In terms of callus induction and subsequent plant regeneration, cotyledon explants were more responsive than hypocotyl explants. Regenerated shoots (2-3 cm) were rooted on MS hormone-free medium or medium containing 0.1 mg/l indole-3-butyric acid. About 90% of regenerated plantlets survived under field conditions after hardening in the glasshouse. Several somaclones exhibiting useful variation would to be proposed as initial plant material for eggplant breeding programs.
Cloning, purification and characterization of the ribosomal protein L11 from E. coli  [PDF]
Roumiana Todorova
American Journal of Molecular Biology (AJMB) , 2011, DOI: 10.4236/ajmb.2011.11005
Abstract: A high-expression system of L11 was constructed and investigated its interaction with other elements of the ribosome using physicochemical methods. The gene rplK, coding for the protein L11 from the E. coli 50S ribosomal subunit was amplifyied, cloned and over-expressed. The protein L11 was purified under native and denaturing conditions, refolded and the structure of both proteins was compared. The protein L11 properly refolded from 6M urea after dialysis. Experiments on binding of proteins L11, RRF and EF-G from Escherichia coli were performed by ana-lytical centrifugation and Biacore. Specific binding between protein L11 and RRF by analytical cen-trifugation was not detected probably due to struc-tural reasons. These findings may be helpful in the design of new antibiotics that specifically disrupt the interactions in the “GTP-associated site” of the bac-terial ribosome, as many of them are not effective anymore. A common intrinsically disordered region of protein L11 was found to be the amino acid se-quence 86-97, while the residues 67-74, containing the linker region, are predicted to be disordered by DisEMBL.
Disorder structural predictions of the native EWS and its oncogenic fusion proteins in rapport with the function  [PDF]
Roumiana Todorova
Advances in Bioscience and Biotechnology (ABB) , 2012, DOI: 10.4236/abb.2012.31005
Abstract: The Intrinsic structural disorder (ISD) of native EWS and its fusion oncogenic proteins, including EWS/FliI, EWS/ATF1 and EWS/ZSG, was estimated by different Predictors. The ISD difference between the wild type and the oncogenic fusions found in the CTD is due to the fusion partner, usually a transcription factor (TF). A disordered region was found in the sequence (AA 132 - 156) of the NTD (EAD) of EWS, consisting of the longest region free of Y motifs. The IQ domain (AA 258 - 280), a Y-free region, flanked by two Y-boxes, is also disordered by all used Predictors. The EWS functional regions RGG1, RGG2 and RGG3 are predominantly disordered. A strong dependence was found between the structure of EWS protein and its oncogenic fusions, and their estimated ISD. The oncogenic function of the fusions is related to a decreased ISD in the CTD, due to the fused TF. The Predictors shown that the different isoforms have similar profiles, shifted with some amino acids, due to the translocations. On the bases of the prediction results, an analysis was made of the EWS sequence and its functional regions with increased ISD to make a relationship sequence-disorder-function that could be helpful in the design of antitumor agents against the corresponding malignances.
Diagnostic Strategies and Treatment for Ewing’s Sarcoma  [PDF]
Roumiana Todorova, Atanas T. Atanasov
International Journal of Clinical Medicine (IJCM) , 2012, DOI: 10.4236/ijcm.2012.36097
Abstract: Ewing’s sarcoma is an enigmatic malignancy of progenitor cell origin, driven by transcription factor oncogenic fusions. About 85% of ESFT cases harbor the t(11;22) translocation and express the fusion protein EWS-FLI. Both bone marrow-derived human Mesenchymal stem cells and Neural crest stem cells are permissive for EWS-FLI1 expression that initiates transition to ESFT-like cellular phenotype. Diagnosis of Ewing’s tumor is based on pathologic and molecular findings. The hypoxia enhances the malignancy of ESFT invasive capacity. An ALDHhigh subpopulation of Ewing’s sarcoma cells, capable of self-renewal, tumor initiation and resistant to chemotherapy in vitro, are not resistant to YK-4-279. Intensive high-dose chemotherapy followed by stem-cell reconstitution was used for ESFT patients in second remission. Plerixafor in combination with G-CSF is an effective enhance stem cell mobilization regimen for stem cell collection with lowest success rate in patients with neuroblastoma. The ESFT-derived antigens EZH2(666) and CHM1(319) are suitable targets for protective allo-restricted human CD8(+) T-cell responses against non-immunogenic ESFT. Primitive neuroectodermal features and MSC origin are both compatible with G(D2) aberrant expression and explore G(D2) immune targeting in ESFT.
Functional Interactions in Transcription and Splicing of Ewing’s Sarcoma
Roumiana Todorova
ISRN Genetics , 2013, DOI: 10.5402/2013/184063
Abstract: Ewing’s sarcoma (EWS) protein is a member of the TET (TLS/EWS/TAF15) family of RNA and DNA-binding proteins with unknown cellular role. EWS protein is encoded by the EWS oncogene on chromosome 22q12, a target of chromosomal translocations in Ewing’s sarcoma tumors. The exact mechanism of EWS participation in gene expression and pathogenesis of the resulting cancers is not defined. The binding partners of native EWS and EWS fusion proteins (EFPs) are described schematically in a model, an attempt to link the transcription with the splicing. The experimental data about the partnerships of EWS and EFPs are summarized, which may lead to better understanding of their function. 1. Introduction Transcription and splicing seems to be connected by proteins with roles in both processes, coordinating them, such as TET proteins, since their NTDs mediate interactions with RNA polymerase II (Pol II), while their CTD binds to splicing factors. Thus TET proteins may recruit splicing factors to the Pol II, which coordinates pre-mRNA processing events [1]. The participation of native Ewing’s sarcoma protein (EWS) and its oncogenic fusion proteins (EFPs), as well as their reported binding partners in transcription and splicing, could be described schematically by a model to link the transcription with the splicing in ESFTs. Some EWS and EWS/FLI1 interacting partners (including Pol II subunits) are implicated in transcriptome and spliceosome and are directly involved in mRNA synthesis or splicing. 1.1. Ewing’s Sarcoma Ewing’s sarcoma, first described by James Ewing in 1921, is still a cryptic malignancy. Ewing’s sarcoma family tumors (ESFTs) afflict children and young adults, encompassing Ewing’s Sarcoma of bone, extraosseous (soft-tissue) Ewing’s sarcoma, primitive neuroectodermal Tumor (PNET), and Askin’s tumor. ESFTs have high propensity to metastasize in bone, bone marrow, and lung. ESFTs are aggressive round cell tumors of putative stem cell origin, for which prognostic biomarkers and novel treatments are needed [2, 3]. ESFTs are chemotherapy-sensitive cancers, and even patients with metastatic disease commonly achieve remission. Diagnosis of Ewing tumor is based on pathologic and molecular findings [4]. The EFPs are promoter-specific transcriptional activators, due to EWS-activation domain (EAD) and a DNA-binding domain (DBD) from the fusion partner. About 85% of Ewing tumours carry the most frequent EWSR1/FLI1 fusion gene that is critically important for maintaining the tumor phenotype of the disease. The EWS/FLI1 may be fully transforming only in a mutated cell
Faster Replacement Paths
Virginia Vassilevska Williams
Computer Science , 2010,
Abstract: The replacement paths problem for directed graphs is to find for given nodes s and t and every edge e on the shortest path between them, the shortest path between s and t which avoids e. For unweighted directed graphs on n vertices, the best known algorithm runtime was \tilde{O}(n^{2.5}) by Roditty and Zwick. For graphs with integer weights in {-M,...,M}, Weimann and Yuster recently showed that one can use fast matrix multiplication and solve the problem in O(Mn^{2.584}) time, a runtime which would be O(Mn^{2.33}) if the exponent \omega of matrix multiplication is 2. We improve both of these algorithms. Our new algorithm also relies on fast matrix multiplication and runs in O(M n^{\omega} polylog(n)) time if \omega>2 and O(n^{2+\eps}) for any \eps>0 if \omega=2. Our result shows that, at least for small integer weights, the replacement paths problem in directed graphs may be easier than the related all pairs shortest paths problem in directed graphs, as the current best runtime for the latter is \Omega(n^{2.5}) time even if \omega=2.
Investigation of the Potential of Near Infrared Spectroscopy for the Detection and Quantification of Pesticides in Aqueous Solution  [PDF]
Aoife A. Gowen, Yutaro Tsuchisaka, Colm O’Donnell, Roumiana Tsenkova
American Journal of Analytical Chemistry (AJAC) , 2011, DOI: 10.4236/ajac.2011.228124
Abstract: This research investigates the potential of near infrared spectroscopy (NIRS) for the detection and quantification of pesticides in aqueous solution. Standard solutions of Alachlor and Atrazine (ranging in concentration from 1.25 - 100 ppm) were prepared by dilution in a Methanol/water solvent (1:1 methanol/water (v/v)). Near infrared transmission spectra were obtained in the wavelength region 400 - 2500 nm; however, the wavelength regions below 1300 nm and above 1900 nm were omitted in subsequent analysis due to the poor signal repeatability in these regions. Partial least squares analysis was applied for discrimination between pesticide and solvent and for prediction of pesticide concentration. Limits of detection of 12.6 ppm for Alachlor and 46.4 ppm for Atrazine were obtained.
Minimum Weight Cycles and Triangles: Equivalences and Algorithms
Liam Roditty,Virginia Vassilevska Williams
Computer Science , 2011,
Abstract: We consider the fundamental algorithmic problem of finding a cycle of minimum weight in a weighted graph. In particular, we show that the minimum weight cycle problem in an undirected n-node graph with edge weights in {1,...,M} or in a directed n-node graph with edge weights in {-M,..., M} and no negative cycles can be efficiently reduced to finding a minimum weight triangle in an Theta(n)-node undirected graph with weights in {1,...,O(M)}. Roughly speaking, our reductions imply the following surprising phenomenon: a minimum cycle with an arbitrary number of weighted edges can be "encoded" using only three edges within roughly the same weight interval! This resolves a longstanding open problem posed by Itai and Rodeh [SIAM J. Computing 1978 and STOC'77]. A direct consequence of our efficient reductions are O (Mn^{omega})-time algorithms using fast matrix multiplication (FMM) for finding a minimum weight cycle in both undirected graphs with integral weights from the interval [1,M] and directed graphs with integral weights from the interval [-M,M]. The latter seems to reveal a strong separation between the all pairs shortest paths (APSP) problem and the minimum weight cycle problem in directed graphs as the fastest known APSP algorithm has a running time of O(M^{0.681}n^{2.575}) by Zwick [J. ACM 2002]. In contrast, when only combinatorial algorithms are allowed (that is, without FMM) the only known solution to minimum weight cycle is by computing APSP. Interestingly, any separation between the two problems in this case would be an amazing breakthrough as by a recent paper by Vassilevska W. and Williams [FOCS'10], any O(n^{3-eps})-time algorithm (eps>0) for minimum weight cycle immediately implies a O(n^{3-delta})-time algorithm (delta>0) for APSP.
Popular conjectures imply strong lower bounds for dynamic problems
Amir Abboud,Virginia Vassilevska Williams
Computer Science , 2014,
Abstract: We consider several well-studied problems in dynamic algorithms and prove that sufficient progress on any of them would imply a breakthrough on one of five major open problems in the theory of algorithms: 1. Is the 3SUM problem on $n$ numbers in $O(n^{2-\epsilon})$ time for some $\epsilon>0$? 2. Can one determine the satisfiability of a CNF formula on $n$ variables in $O((2-\epsilon)^n poly n)$ time for some $\epsilon>0$? 3. Is the All Pairs Shortest Paths problem for graphs on $n$ vertices in $O(n^{3-\epsilon})$ time for some $\epsilon>0$? 4. Is there a linear time algorithm that detects whether a given graph contains a triangle? 5. Is there an $O(n^{3-\epsilon})$ time combinatorial algorithm for $n\times n$ Boolean matrix multiplication? The problems we consider include dynamic versions of bipartite perfect matching, bipartite maximum weight matching, single source reachability, single source shortest paths, strong connectivity, subgraph connectivity, diameter approximation and some nongraph problems such as Pagh's problem defined in a recent paper by Patrascu [STOC 2010].
Quantum algorithms for shortest paths problems in structured instances
Aran Nayebi,Virginia Vassilevska Williams
Computer Science , 2014,
Abstract: We consider the quantum time complexity of the all pairs shortest paths (APSP) problem and some of its variants. The trivial classical algorithm for APSP and most all pairs path problems runs in $O(n^3)$ time, while the trivial algorithm in the quantum setting runs in $\tilde{O}(n^{2.5})$ time, using Grover search. A major open problem in classical algorithms is to obtain a truly subcubic time algorithm for APSP, i.e. an algorithm running in $O(n^{3-\varepsilon})$ time for constant $\varepsilon>0$. To approach this problem, many truly subcubic time classical algorithms have been devised for APSP and its variants for structured inputs. Some examples of such problems are APSP in geometrically weighted graphs, graphs with small integer edge weights or a small number of weights incident to each vertex, and the all pairs earliest arrivals problem. In this paper we revisit these problems in the quantum setting and obtain the first nontrivial (i.e. $O(n^{2.5-\varepsilon})$ time) quantum algorithms for the problems.
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