data protein interaction data and ontology based literature searches

... of a protein directly depend on its three-dimensional structure The understanding of protein is the understanding its sequence, structure and function Therefore, studying of protein-protein interaction ... protein blocks and random under-sampling technique i For the predicting protein-protein interaction sites problem, experimental results on the dataset that contains 2,829 interface residues and ... interact, and to predict which proteins interact with which others The first problem is called protein-protein interaction sites prediction Learning about this issue leads to the understanding how proteins...

Ngày tải lên: 20/05/2016, 16:03

... extend the hand-curated pathway from 73 proteins and 187 interactions to 181 proteins and 768 interactions A total of 581 FIs were added between pathway components and new mutated protein interactions ... (TGFβ) pathway consists of a ligand receptor binding event that initiates a series of protein-protein interaction (PPI), protein degradation, protein phosphorylation, and protein-DNA binding events ... Human Protein Reference Database (HPRD) [31], I2D [32], IntACT [33], and MINT [34], and expression data sets from the Stanford Microarray Database [35] and the Gene Expression Omnibus [36] Protein...

Ngày tải lên: 09/08/2014, 20:22

... homology-based predictions, namely on the one hand side MAKER2 using exonerate and on the other hand side GeMoMa without RNA-seq data In all cases, we use the same reference species and reference proteins ... conservation, intron position conservation and optionally RNA-seq data for homology-based gene prediction We show on published benchmark data for plants, animals and fungi that GeMoMa performs better ... prediction based on general features of (protein-coding) genes [3, 4], and homology-based gene prediction relying on gene models of (closely) related, well-annotated species [5–7] Experimental data...

Ngày tải lên: 25/11/2020, 15:53

... species, and it now suffices to generate partial protein sequence information with which to access entire (predicted) protein sequences stored in expressed sequence tag, gene and protein sequence databases. This ... post-translational modifica- tions ) protein processing [34,36] and N-glycosylation [39] – and describe the use of COFRADIC for study- ing interactions between small molecules and proteins. The latter is ... to further analysis. Affinity-based isolation of N-glycosylated proteins is rather simple and is based on lectin-affinity chromatography. Lectins are proteins or glycoproteins that recognize oligosaccharides...

Ngày tải lên: 18/02/2014, 16:20

... compilation ª 2006 FEBS 1331 and non-native states of targeted proteins, but how they discriminate between correctly and incorrectly folded proteins and how they selectively retain and tar- get the latter ... Gaucher’s disease and many other degenerative and neurodegenerative disorders. Cellular mole- cular chaperones, which are ubiquitous, stress-induced proteins, and newly found chemical and pharmacological ... REVIEW ARTICLE Protein-misfolding diseases and chaperone-based therapeutic approaches Tapan K. Chaudhuri and Subhankar Paul Department of Biochemical Engineering and Biotechnology, Indian...

Ngày tải lên: 07/03/2014, 12:20

... galactose-terminated glycoproteins and neoglycoproteins with high affinity Bound ligands are internalized by the cell via receptor-mediated endocytosis Due to its specificity, the asialoglycoprotein receptor ... Posttranslational processing results in the RNA binding nucleocapsid protein C, the envelope proteins E1 and E2, and the nonstructural proteins NS1 to NS5, including RNA-dependent RNA polymerase At ... delivery of protein DNA complexes is the use of asialoglycoprotein receptors The asialoglycoprotein receptor is present in large numbers only on the plasma membrane of hepatocytes and binds galactose-terminated...

Ngày tải lên: 10/04/2014, 22:11

... Gaucher disease [20,21], Tay-Sachs and Sandhoff disease [22] (details for Gaucher and Tay-Sachs ⁄ Sandhoff diseases are reviewed separately), GM1-gangliosidosis [23], and retinitis pigmentosa 17 [24] ... N215S, Q279E, M296I, and M296V), four mutations found in classic patients (E59K, A156V, L166V, and R356W), and two mutations present in both variant and classic patients (A97V and R301Q) were efficiently ... with D92, D93, K168, E203, R227, and E231; and a hydrophobic surface on DGJ makes van der Waals interactions with W47 (Fig 4) The binding between DGJ and the protein would fix the active-site...

Ngày tải lên: 30/03/2014, 03:20

... factors such as flt-3 ligand and megakaryocyte growth and development factor (MGDF)/thrombopoietin (TPO) have augmented the level of genetically modified cells These cytokines and growth factors maintain ... retroviral vector containing Neo and human ADA genes in both murine and human T lymphocytes Transduced murine lymphocytes could be selected by growth in G418 and subsequently expanded without changing ... cells However, CD24 and HSA are glycosylphophatidylinositol-linked surface proteins This class of proteins has been shown to be transferred from cell to cell both in vitro and in vivo, possibly...

Ngày tải lên: 10/04/2014, 22:10

... E2F is bound to a complex of other proteins, including a protein known as the retinoblastoma (Rb) gene product Rb prevents E2F’s interaction with chromosomal DNA and stimulation of gene activity ... GRAFTS 193 FIGURE 8.4 Control oligonucleotide-treated (A and B) and antisense oligonucleotide (against c and kinase/PCNA)-treated vein grafts (C and D) in hypercholesterolernic rabbits, weeks after ... of sulfhydryl groups of intracellular and membrane proteins, nucleic acid injury, and breakdown of components of the extracellular matrix such as collagen and hyaluronic acid Natural oxygen radical...

Ngày tải lên: 10/04/2014, 22:11

... the viral proteins The HIV genome encodes three sets of viral proteins; the structural proteins (Gag, Pol, and Env), the regulatory proteins (Tat, Rev, and Nef), and the maturation proteins (Vif, ... classes of viral proteins are generated from these mRNAs: structural proteins, regulatory proteins, and maturation proteins The structural proteins include the viral envelope protein (gp 120, ... the physical interaction of the HIV envelope glycoprotein gp120 and the CD4 protein Based on these results, investigators have demonstrated that sCD4 protein can effectively bind to and inhibit...

Ngày tải lên: 10/04/2014, 22:11

... Materials and Methods, and CD11c+ cells were isolated from BAL fluid and lymph nodes Cells were analyzed by flow cytometry for the expression of CD40, CD80, CD86, and I-Ad gated to CD11c+b+ The data ... mice were euthanized and the lungs were removed and fixed in buffered formalin Whole lungs were embedded in paraffin, sectioned, and examined for GFP by fluorescent microscopy, and an approximate ... were treated therapeutically with CIN and then challenged with OVA and euthanized 18 hours later Lungs were removed, and single-cell suspensions were prepared and plated as described above In this...

Ngày tải lên: 08/08/2014, 21:20

... clinical trial In vitro and in vivo Adenovirus Ad5/3-D24 Main result In vitro in vivo In vitro in vivo In vitro in vivo In vitro in vivo In vitro in vivo and and and and and Killing of ovarian ... (Table 2) A plasmid -based strategy with HSV-TK/GCV was assessed in vitro both in human clinical samples and in a rat leiomyoma cell line A bystander effect was demonstrated, and interestingly, ... to perform extensive sampling and biopsies in phase I trials to acquire material for correlative studies Obviously, this is hampered by compliance and cost issues and the fact that traditionally...

Ngày tải lên: 22/03/2014, 11:20

... molecular weights and compositions (comonomer fraction up to 66 mol%) are able to bind DNA, yielding polyplexes (14,15; and Bos and Hennink, unpublished data) However, for random copolymers of ... 3.3.), and by NMR For 1H-NMR assignments, see Subheading 3.1.8 and Notes and 3.3 GPC of pDMAEMA Homo- and Copolymers This instruction is intended for the molecular weight determination of pDMAEMA and ... Sugihara, G (1996) Design and synthesis of amphiphilic -helical model peptides with systematically varied hydrophobic-hydrophilic balance and their interaction with lipid- and bio-membranes Biochemistry...

Ngày tải lên: 11/04/2014, 09:59

... Methods and Protocols, edited by Curtis A Machida, 2003 60 Interleukin Protocols, edited by Luke A J O’Neill and Andrew Bowie, 2001 75 Lung Cancer: Volume 2, Diagnostic and Therapeutic Methods and ... Methods and Protocols, edited by Andrew J Pollard and Martin C J Maiden, 2001 50 Colorectal Cancer: Methods and Protocols, edited by Steven M Powell, 2001 66 Meningococcal Vaccines: Methods and Protocols, ... Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand MARKUS U EHRENGRUBER • Brain Research Institute, University of Zurich, Zurich, Switzerland JOHN F ENGELHARDT...

Ngày tải lên: 11/04/2014, 10:39

... in green genes (ISGs), IFN induced proteins (IIPs), IFN associated signaling pathway molecules, such as JAK and STAT and IFN associated proteins, such as IL18 and OAS molecules (additional file ... quality and concentration were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) First- and second-strand cDNA were synthesized from 12.5 μg of Ad5-CMV-GFP and Ad5-CMV-null ... set of Ad DNA standards (449B plasmid) Plasmids for constructing pISRE-SEAP and pIFN-betaSEAP, and pMetLuc-Control were obtained from Clontech Secreted alkaline phosphatase (SEAP) and secreted luciferase...

Ngày tải lên: 18/06/2014, 16:20

... cells and GM-CSF (TVAX) Later, autologous T cells are harvested and expanded ex vivo, and then administered intravenously Pilot clinical trials showed promising results with this approach to expand ... conceived, outlined the direction of, and drafted the manuscript MJH, CCM and KLE refined the search for information, gathered references and generated the tables and figure MRJ, RMP, LML provided ... being vaccinated with the heat shock protein peptide complex (HSPPC)-96 with or without concurrent TMZ therapy Heat shock proteins (HSP) are highly conserved proteins that are transiently expressed...

Ngày tải lên: 18/06/2014, 16:20

... the experiments and wrote the paper draft; LS conceived, instructed the experiments and revised the paper; SG and XX performed experiments and analyzed data; ZX and ZP collected and validated tissue ... cells, and CD indicated viability of HUVEC cells respectively treated with PCFC-g-PEI and FA-PEAs, which was respectively compared with 25-kD and 2-kD PEI The error bars represented the standard ... image that used PCFC-g-PEI, FA-PEAs and HPEI as a gene delivery vector respectively And figure B, D and F represented the transfection image with 25-kD PEI and 2-kD PEI as gene vectors Figure...

Ngày tải lên: 18/06/2014, 19:20

... Inc., Cleveland, Ohio, USA) to be used in this study is isolated from a single bone marrow aspirate and cultured with heat inactivated fetal bovine serum (FBS) and growth factors EGF and PDGF Cells ... Pre- and Intraoperative Data Patients enrolled in this study will not need to undergo additional screening visits or clinical investigations in addition to standard pre-transplant work-up Standardof-care ... abdominal computed tomography with intravenous and oral contrast, pulmonary function tests, and arterial blood gas analysis Intraoperative data (warm and cold ischemia Popp et al Journal of Translational...

Ngày tải lên: 18/06/2014, 22:20