The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Y Pan - One of the best experts on this subject based on the ideXlab platform.
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construction and application of dynamic protein interaction network based on time course gene expression data
Proteomics, 2013Co-Authors: Jianxin Wang, Xiaoqing Peng, Y PanAbstract:In recent years, researchers have tried to inject dynamic information into static protein interaction networks (PINs). The paper first proposes a three-sigma method to identify active time points of each protein in a cellular cycle, where three-sigma principle is used to compute an active threshold for each gene according to the characteristics of its expression curve. Then a dynamic protein interaction network (DPIN) is constructed, which includes the dynamic changes of protein interactions. To validate the efficiency of DPIN, MCL, CPM, and core attachment algorithms are applied on two different DPINs, the static PIN and the time course PIN (TC-PIN) to detect protein complexes. The performance of each algorithm on DPINs outperforms those on other networks in terms of matching with known complexes, sensitivity, specificity, f-measure, and accuracy. Furthermore, the statistics of three-sigma principle show that 23-45% proteins are active at a time point and most proteins are active in about half of cellular cycle. In addition, we find 94% essential proteins are in the group of proteins that are active at equal or great than 12 timepoints of GSE4987, which indicates the potential existence of feedback mechanisms that can stabilize the expression level of essential proteins and might provide a new insight for predicting essential proteins from dynamic protein networks.
Jun S Liu - One of the best experts on this subject based on the ideXlab platform.
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context specific protein network miner an online system for exploring context specific protein interaction networks from the literature
PLOS ONE, 2012Co-Authors: Rajesh Chowdhary, Sin Lam Tan, Jinfeng Zhang, Shreyas Karnik, Vladimir B Bajic, Jun S LiuAbstract:Background Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis.
Henry Daniell - One of the best experts on this subject based on the ideXlab platform.
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expression of cholera toxin b proinsulin fusion protein in lettuce and tobacco chloroplasts oral administration protects against development of insulitis in non obese diabetic mice
Plant Biotechnology Journal, 2007Co-Authors: Tracey A Ruhlman, Raheleh Ahangari, Andrew L Devine, Mohtahsem Samsam, Henry DaniellAbstract:Lettuce and tobacco chloroplast transgenic lines expressing the cholera toxin B subunit–human proinsulin (CTB-Pins) fusion protein were generated. CTB-Pins accumulated up to ~16% of total soluble protein (TSP) in tobacco and up to ~2.5% of TSP in lettuce. Eight milligrams of powdered tobacco leaf material expressing CTB-Pins or, as negative controls, CTB–green fluorescent protein (CTB-GFP) or interferon–GFP (IFN-GFP), or untransformed leaf, were administered orally, each week for 7 weeks, to 5-week-old female non-obese diabetic (NOD) mice. The pancreas of CTB-Pins-treated mice showed decreased infiltration of cells characteristic of lymphocytes (insulitis); insulin-producing β-cells in the pancreatic islets of CTB-Pins-treated mice were significantly preserved, with lower blood or urine glucose levels, by contrast with the few β-cells remaining in the pancreatic islets of the negative controls. Increased expression of immunosuppressive cytokines, such as interleukin-4 and interleukin-10 (IL-4 and IL-10), was observed in the pancreas of CTB-Pins-treated NOD mice. Serum levels of immunoglobulin G1 (IgG1), but not IgG2a, were elevated in CTB-Pins-treated mice. Taken together, T-helper 2 (Th2) lymphocyte-mediated oral tolerance is a likely mechanism for the prevention of pancreatic insulitis and the preservation of insulin-producing β-cells. This is the first report of expression of a therapeutic protein in transgenic chloroplasts of an edible crop. Transplastomic lettuce plants expressing CTB-Pins grew normally and transgenes were maternally inherited in T1 progeny. This opens up the possibility for the low-cost production and delivery of human therapeutic proteins, and a strategy for the treatment of various other autoimmune diseases.
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expression of cholera toxin b proinsulin fusion protein in lettuce and tobacco chloroplasts oral administration protects against development of insulitis in non obese diabetic mice
Plant Biotechnology Journal, 2007Co-Authors: Tracey A Ruhlman, Raheleh Ahangari, Andrew L Devine, Mohtahsem Samsam, Henry DaniellAbstract:Lettuce and tobacco chloroplast transgenic lines expressing the cholera toxin B subunit-human proinsulin (CTB-Pins) fusion protein were generated. CTB-Pins accumulated up to ~16% of total soluble protein (TSP) in tobacco and up to ~2.5% of TSP in lettuce. Eight milligrams of powdered tobacco leaf material expressing CTB-Pins or, as negative controls, CTB-green fluorescent protein (CTB-GFP) or interferon-GFP (IFN-GFP), or untransformed leaf, were administered orally, each week for 7 weeks, to 5-week-old female non-obese diabetic (NOD) mice. The pancreas of CTB-Pins-treated mice showed decreased infiltration of cells characteristic of lymphocytes (insulitis); insulin-producing beta-cells in the pancreatic islets of CTB-Pins-treated mice were significantly preserved, with lower blood or urine glucose levels, by contrast with the few beta-cells remaining in the pancreatic islets of the negative controls. Increased expression of immunosuppressive cytokines, such as interleukin-4 and interleukin-10 (IL-4 and IL-10), was observed in the pancreas of CTB-Pins-treated NOD mice. Serum levels of immunoglobulin G1 (IgG1), but not IgG2a, were elevated in CTB-Pins-treated mice. Taken together, T-helper 2 (Th2) lymphocyte-mediated oral tolerance is a likely mechanism for the prevention of pancreatic insulitis and the preservation of insulin-producing beta-cells. This is the first report of expression of a therapeutic protein in transgenic chloroplasts of an edible crop. Transplastomic lettuce plants expressing CTB-Pins grew normally and transgenes were maternally inherited in T(1) progeny. This opens up the possibility for the low-cost production and delivery of human therapeutic proteins, and a strategy for the treatment of various other autoimmune diseases.
Rajesh Chowdhary - One of the best experts on this subject based on the ideXlab platform.
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context specific protein network miner an online system for exploring context specific protein interaction networks from the literature
PLOS ONE, 2012Co-Authors: Rajesh Chowdhary, Sin Lam Tan, Jinfeng Zhang, Shreyas Karnik, Vladimir B Bajic, Jun S LiuAbstract:Background Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis.
Tracey A Ruhlman - One of the best experts on this subject based on the ideXlab platform.
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expression of cholera toxin b proinsulin fusion protein in lettuce and tobacco chloroplasts oral administration protects against development of insulitis in non obese diabetic mice
Plant Biotechnology Journal, 2007Co-Authors: Tracey A Ruhlman, Raheleh Ahangari, Andrew L Devine, Mohtahsem Samsam, Henry DaniellAbstract:Lettuce and tobacco chloroplast transgenic lines expressing the cholera toxin B subunit–human proinsulin (CTB-Pins) fusion protein were generated. CTB-Pins accumulated up to ~16% of total soluble protein (TSP) in tobacco and up to ~2.5% of TSP in lettuce. Eight milligrams of powdered tobacco leaf material expressing CTB-Pins or, as negative controls, CTB–green fluorescent protein (CTB-GFP) or interferon–GFP (IFN-GFP), or untransformed leaf, were administered orally, each week for 7 weeks, to 5-week-old female non-obese diabetic (NOD) mice. The pancreas of CTB-Pins-treated mice showed decreased infiltration of cells characteristic of lymphocytes (insulitis); insulin-producing β-cells in the pancreatic islets of CTB-Pins-treated mice were significantly preserved, with lower blood or urine glucose levels, by contrast with the few β-cells remaining in the pancreatic islets of the negative controls. Increased expression of immunosuppressive cytokines, such as interleukin-4 and interleukin-10 (IL-4 and IL-10), was observed in the pancreas of CTB-Pins-treated NOD mice. Serum levels of immunoglobulin G1 (IgG1), but not IgG2a, were elevated in CTB-Pins-treated mice. Taken together, T-helper 2 (Th2) lymphocyte-mediated oral tolerance is a likely mechanism for the prevention of pancreatic insulitis and the preservation of insulin-producing β-cells. This is the first report of expression of a therapeutic protein in transgenic chloroplasts of an edible crop. Transplastomic lettuce plants expressing CTB-Pins grew normally and transgenes were maternally inherited in T1 progeny. This opens up the possibility for the low-cost production and delivery of human therapeutic proteins, and a strategy for the treatment of various other autoimmune diseases.
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expression of cholera toxin b proinsulin fusion protein in lettuce and tobacco chloroplasts oral administration protects against development of insulitis in non obese diabetic mice
Plant Biotechnology Journal, 2007Co-Authors: Tracey A Ruhlman, Raheleh Ahangari, Andrew L Devine, Mohtahsem Samsam, Henry DaniellAbstract:Lettuce and tobacco chloroplast transgenic lines expressing the cholera toxin B subunit-human proinsulin (CTB-Pins) fusion protein were generated. CTB-Pins accumulated up to ~16% of total soluble protein (TSP) in tobacco and up to ~2.5% of TSP in lettuce. Eight milligrams of powdered tobacco leaf material expressing CTB-Pins or, as negative controls, CTB-green fluorescent protein (CTB-GFP) or interferon-GFP (IFN-GFP), or untransformed leaf, were administered orally, each week for 7 weeks, to 5-week-old female non-obese diabetic (NOD) mice. The pancreas of CTB-Pins-treated mice showed decreased infiltration of cells characteristic of lymphocytes (insulitis); insulin-producing beta-cells in the pancreatic islets of CTB-Pins-treated mice were significantly preserved, with lower blood or urine glucose levels, by contrast with the few beta-cells remaining in the pancreatic islets of the negative controls. Increased expression of immunosuppressive cytokines, such as interleukin-4 and interleukin-10 (IL-4 and IL-10), was observed in the pancreas of CTB-Pins-treated NOD mice. Serum levels of immunoglobulin G1 (IgG1), but not IgG2a, were elevated in CTB-Pins-treated mice. Taken together, T-helper 2 (Th2) lymphocyte-mediated oral tolerance is a likely mechanism for the prevention of pancreatic insulitis and the preservation of insulin-producing beta-cells. This is the first report of expression of a therapeutic protein in transgenic chloroplasts of an edible crop. Transplastomic lettuce plants expressing CTB-Pins grew normally and transgenes were maternally inherited in T(1) progeny. This opens up the possibility for the low-cost production and delivery of human therapeutic proteins, and a strategy for the treatment of various other autoimmune diseases.
