Nodal and BMP signaling pathways network with WNT signaling pathway during
embryogenesis and carcinogenesis. CER1 (Cerberus 1) and GREM3 (CKTSF1B3 or CER2)
inhibit NODAL signaling through ACVR1B ...(ALK4) or ACVR1C (ALK7) to SMAD2 or SMAD3.
GREM1 (CKTSF1B1) inhibits BMP signaling through BMPR1A (ALK3), BMPR1B (ALK6) or
ACVR1 (ALK2) to SMAD1, SMAD5 or SMAD8. CER1, GREM1 and GREM3 are DAN domain (DAND)
family members; however, transcriptional regulation of DAND family members by
canonical WNT signaling pathway remains unclear. We searched for the TCF/LEF-binding
site within the promoter region of DAND family genes, including CER1, GREM1, GREM2,
GREM3 and NBL1. Because triple TCF/LEF-binding sites were identified within human
CER1 promoter by using bioinformatics and human intelligence, comparative genomics
analyses on CER1 orthologs were further performed. Chimpanzee CER1 gene, encoding
267-amino-acid protein, was identified within NW_111298.1 genome sequence. XM_528542.1
was not a correct coding sequence for chimpanzee CER1. Primate CER1 orthologs
were significantly divergent from rodent Cer1 orthologs. Three TCF/LEF-binding
sites within human CER1 promoter were conserved in chimpanzee CER1 promoter, two
in cow and dog Cer1 promoters, but not in rodent Cer1 promoters. Binding sites
for NODAL signaling effectors, SMAD3/SMAD4 and FOXH1, were also conserved among
human, chimpanzee, cow and dog CER1 promoters. CER1 orthologs were evolutionarily
conserved target of WNT and NODAL signaling pathways in non-rodent mammals. Human
CER1 mRNA was expressed in embryonic stem (ES) cells in the undifferentiated state
and in the early endodermal lineage. CER1 upregulation in human ES cells leads
to Nodal signaling inhibition associated with differentiation of human ES cells.
Primate CER1 orthologs, playing a pivotal role during early embryogenesis, underwent
protein evolution as well as promoter evolution. These facts indicate that molecular
evolution of CER1 orthologs contributes to the significantly divergent scenarios
of early embryogenesis in primates and rodents.
Two-dimensional difference in-gel electrophoresis (2D-DIGE) is a modified 2D electrophoresis (2DE) technique that enables comparison of two (or three) proteomes simultaneously on the same gel. The ...different protein samples to be compared are covalently tagged with spectrally different fluorescent dyes that are designed to have no effect on the relative migration of proteins during isoelectric focusing or molecular mass separation during electrophoresis. The “spot maps” generated from the dye scans for each of the dyes are then superimposed to discern the expression pattern of the proteome samples being compared. Proteins that do not change in expression are seen as spots with a fixed ratio of fluorescent signals, whereas proteins that differ between the samples have different fluorescence ratios. The fluorescent dyes used in DIGE are cyanine flours and matched in respect of molecular weight. Two different dye chemistries are available enabling fluorescent tagging of as low as 5 μ g of proteins to get the analysis of the regulation of the proteome. Furthermore, DIGE is a sensitive technique, capable of detecting as little as 0.5 fmol of protein, and this detection system is linear over a >10,000-fold concentration range.
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FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The CNS immune response to rabies virus has been shown to be influenced by virulence of the virus strains. There is no comprehensive report of the peripheral immune response against different strains ...of rabies virus. In this report we used a comparative proteome analysis to find the early events in the spleen lymphocytes of mice infected by a street strain and an attenuated strain of the rabies virus. Differentially expressed proteins were identified which play important biological roles such as T and B lymphocyte activation (coronin 1), antiviral activity (peroxiredoxin 1), and cytoskeletal reorganization (cofilin 1). These results could be strong hints of early divergence on peripheral immune response under influence of viral strain and their pathogenicity.
In this study, we have used Ki‐67 and MF20 mAb to determine how extensively cardiomyocytes proliferate in the postnatal mouse heart. It was established that the cardiomyocytes divided rapidly in ...2‐day‐old hearts. However, at 13 days, the majority of cardiomyocytes had entered into terminal growth arrest and differentiation. We exploited this finding in order to identify proteins that were associated with cardiomyocyte growth and differentiation. The protein profiles of 2‐ and 13‐day‐old hearts were established by two‐dimensional electrophoresis and compared. Seventeen protein spots were found to be differentially expressed at day 13. Eight of them were up‐regulated while the remaining nine protein spots were down‐regulated. We focused our attention on 2 of the proteins identified by MALDI‐TOF MS, cyclin I and p53, because they are both believed to be involved in cell cycle regulation. Western blot analysis confirmed that both proteins were positively up‐regulated in the 13‐day‐old postnatal heart. To determine directly whether these proteins were associated with cell proliferation, we examined their expression patterns in H9c2 cardiomyocytes maintained in vitro. We established that cyclin I expression was low during the growing phase of H9c2 culture and high during the growth arrest/differentiation phases. In contrast, p53 expression was unchanged during both phases. The various growth phases were confirmed by the presence of cyclin A and growth arrest‐specific 1 proteins. We investigated whether silencing cyclin I expression using cyclin I‐siRNA could promote an increase in H9c2 cell proliferation. It was determined that silencing cyclin I could enhance a small, but significant, increase in H9c2 cell division. Similar results were obtained for cardiomyocytes extracted from 13‐day‐old hearts. These results imply that the reason why cardiomyocytes in 13‐day‐old hearts increased cyclin I expression was probably associated with terminal growth arrest. However, the increase in p53 expression was probably associated with cardiomyocyte differentiation, rather than growth arrest.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Host–pathogen interactions are complex competitions during which both the host and the pathogen adapt rapidly to each other in order for one or the other to survive. Salmonella enterica serovar ...Typhimurium is a pathogen with a broad host range that causes a typhoid fever-like disease in mice and severe food poisoning in humans. The murine typhoid fever is a systemic infection in which S. typhimurium evades part of the immune system by replicating inside macrophages and other cells. The transition from a foodborne contaminant to an intracellular pathogen must occur rapidly in multiple, ordered steps in order for S. typhimurium to thrive within its host environment. Using S. typhimurium isolated from rich culture conditions and from conditions that mimic the hostile intracellular environment of the host cell, a native low molecular weight protein fraction, or peptidome, was enriched from cell lysates by precipitation of intact proteins with organic solvents. The enriched peptidome was analyzed by both LC–MS/MS and LC–MS-based methods, although several other methods are possible. Pre-fractionation of peptides allowed identification of small proteins and protein degradation products that would normally be overlooked. Comparison of peptides present in lysates prepared from Salmonella grown under different conditions provided a unique insight into cellular degradation processes as well as identification of novel peptides encoded in the genome but not annotated. The overall approach is detailed here as applied to Salmonella and is adaptable to a broad range of biological systems.
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FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Agarose based immobilized copper (II) affinity chromatography (Cu(II)-IMAC) in tandem with reversed-phase chromatography was applied to a yeast protein extract. Histidine-rich peptides were selected ...and, in the process, samples were substantially simplified prior to mass spectral analysis. Samples of proteins from the yeast extract at fermentation time periods of 2.5 and 10 h were compared quantitatively used the GIST protocol. Acylation of the N-terminus of tryptic peptides with N-acetoxysuccinamide was used to globally label and quantify relative protein concentration changes. Together with N-terminal acylation, an imidazole elution procedure allowed histidine-rich peptides to be preferentially selected by Cu(II)-IMAC. An inverse labeling strategy was applied to increase reliability in determinations of up- and down-regulation. It was found that the concentration of some histidine-rich proteins changed in excess of 4-fold during fermentation. These proteins covered a wide range of molecular weight and pI values. Keywords: Cu(II)-IMAC • histidine-rich peptides • inverse labeling • N-terminus derivatization • yeast • comparative proteomics
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IJS, KILJ, NUK, PNG, UL, UM
VEGF, Hedgehog, FGF, Notch, and WNT signaling pathways network together for vascular remodeling during embryogenesis, tissue regeneration, and carcinogenesis. VEGFA (VEGF), VEGFB, VEGFC, VEGFD (FIGF) ...and PGF (PlGF) are VEGF family ligands for receptor tyrosine kinases, including VEGFR1 (FLT1), VEGFR2 (KDR) and VEGFR3 (FLT4). Bevacizumab (Avastin), Sunitinib (Sutent) and Sorafenib (Nexavar) are anti-cancer drugs targeted to VEGF signaling pathway. TCF/LEF binding sites within the promoter region of human VEGF family members were searched for by using bioinformatics and human intelligence (Humint). Because four TCF/LEF-binding sites were identified within the 5'-promoter region of human VEGFD gene within AC095351.5 genome sequence, comparative genomics analyses on VEGFD orthologs were further performed. ASB9-ASB11-VEGFD locus at human chromosome Xp22.2 and ASB5-VEGFC locus at human chromosome 4q34 were paralogous regions within the human genome. Human VEGFD mRNA was expressed in lung, small intestine, uterus, breast, neural tissues, and neuroblastoma. Mouse Vegfd mRNA was expressed in kidney, pregnant oviduct, and neural tissues. Chimpanzee VEGFD promoter, cow Vegfd promoter, mouse Vegfd promoter and rat Vegfd promoter were identified within NW_121675.1, AC161065.2, AL732475.6 and AC130036.3 genome sequences, respectively. Three out of four TCF/LEF-binding sites within human VEGFD promoter were conserved in chimpanzee VEGFD promoter, and one in cow Vegfd promoter. TCF/LEF-binding site, not conserved in human VEGFD promoter, occurred in cow, mouse and rat Vegfd promoters. At least five out of six bHLH-binding sites within human VEGFD proximal promoter region were conserved in chimpanzee VEGFD proximal promoter region, while only one in cow Vegfd proximal promoter region. Together these facts indicate that relatively significant promoter evolution occurred among mammalian VEGFD orthologs. Human VEGFD was characterized as a potent target gene of WNT/beta-catenin signaling pathway. VEGFD, implicated in angiogenesis and lymphatic metastasis, is a pharmacogenomics target in the field of oncology.
Taking super-rice Liangyoupeijiu as test material, and by the method of two-dimensional gel electrophoresis (2-DE), this paper studied the changes in the leaf and grain proteomics of the variety at ...its late growth stage under different levels of nitrogen fertilization (1/2 times of normal nitrogen level, 20 mg x L(-1); normal nitrogen level, 40 mg x L(-1); 2 times of normal nitrogen level, 80 mg x L(-1)), with the biological functions of 16 leaf proteins, 9 inferior grain proteins, and 4 superior grain proteins identified and analyzed. Nitrogen fertilization could affect and regulate the plant photosynthesis via affecting the activation of photosynthesis-related enzymes and of CO2, the light system unit, and the constitution of electron transfer chain at the late growth stage of the variety. It could also promote the expression of the enzymes related to the energy synthesis and growth in inferior grains. High nitrogen fertilization level was not beneficial to the synthesis of starch in superior grain, but suf
EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHA10, EPHB1, EPHB2, EPHB3, EPHB4 and EPHB6 are EPH family receptors for Ephrin family ligands. Ephrin/EPH signaling pathway networks with the ...WNT signaling pathway during embryogenesis, tissue regeneration, and carcinogenesis. TCF/LEF-binding sites within the promoter region of human EPH family members were searched for by using bioinformatics and human intelligence. Because five TCF/LEF-binding sites were identified within the 5'-promoter region of the EPHA7 gene, comparative genomics analyses on EPHA7 orthologs were further performed. EPHA7-MANEA-FHL5 locus at human chromosome 6q16.1 and EPHA10-MANEAL-FHL3 locus at human chromosome 1p34.3 were paralogous regions within the human genome. Human EPHA7 mRNA was expressed in embryonic stem (ES) cells, neural tissues, duodenal cancer and parathyroid tumors, while mouse Epha7 mRNA was expressed in fertilized egg, Rathke's pouche, visual cortex, pituitary gland, other neural tissues, pancreas, lung tumors and mammary tumors. The chimpanzee EPHA7 gene and cow Epha7 gene were identified within NW_107969.1 and AC155055.2 genome sequences, respectively. Five TCF/LEF-binding sites within human EPHA7 promoter were conserved in the chimpanzee EPHA7 promoter, and three TCF/LEF-binding sites in the cow Epha7 promoter, but none in the mouse Epha7 promoter. Primates and cow EPHA7 orthologs were identified as evolutionarily conserved targets of the WNT/beta-catenin signaling pathway. D6S1056 microsatellite marker within EPHA7 gene is deleted in prostate cancer. Deletion and/or promoter CpG hypermethylation could explain the EPHA7 down-regulation in human tumors. EPHA7 is a target of systems medicine, especially in the fields of regenerative medicine and oncology.
The yield of microalgae biomass is the key to affect the accumulation of fatty acids. A few microalgae can assimilate organic carbon to improve biomass yield. In mixotrophic cultivation, microalgae ...can use organic carbon source and light energy simultaneously. The preference of the main energy source by microalgae determines the biomass yield.
is an oleaginous mixotrophic microalga that can efficiently assimilate glucose and accumulate a large amount of biomass and fatty acids. The current study focused on the effect of light on the growth and glucose assimilation of
.
In this study, we found that the uptake and metabolism of glucose in
could be inhibited by light, resulting in a reduction of biomass growth and lipid accumulation. We employed comparative proteomics to study the influence of light on the regulation of glucose assimilation in
. Proteomics revealed that proteins involving in gene translation and photosynthesis system were up-regulated in the light, such as ribulose-phosphate 3-epimerase and phosphoribulokinase. Calvin cycle-related proteins were also up-regulated, suggesting that light may inhibit glucose metabolism by enhancing the production of glyceraldehyde-3-phosphate (G3P) in the Calvin cycle. In addition, the redox homeostasis-related proteins such as thioredoxin reductase were up-regulated in the light, indicating that light may regulate glucose uptake by changing the redox balance. Moreover, the increase of NADH levels and redox potential of the medium under illumination might inhibit the activity of the glucose transport system and subsequently reduce glucose uptake.
A theoretical model of how glucose assimilation in
is negatively influenced by light was proposed, which will facilitate further studies on the complex mechanisms underlying the transition from autotrophy to heterotrophy for improving biomass accumulation.
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