scholarly journals Expressed Genome of Methylobacillus flagellatus as Defined through Comprehensive Proteomics and New Insights into Methylotrophy

2010 ◽  
Vol 192 (19) ◽  
pp. 4859-4867 ◽  
Author(s):  
Erik L. Hendrickson ◽  
David A. C. Beck ◽  
Tiansong Wang ◽  
Mary E. Lidstrom ◽  
Murray Hackett ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Genomic Islands ◽  
Oxidation Reactions ◽  
Phosphogluconate Dehydrogenase ◽  
Dehydrogenase Reaction ◽  
Functional Profiling ◽  
Liquid Chromatography Tandem Mass ◽  
Methylotrophic Growth ◽  
Nano Liquid Chromatography ◽  
Protein Expression Profiles

ABSTRACT In recent years, techniques have been developed and perfected for high-throughput identification of proteins and their accurate partial sequencing by shotgun nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS), making it feasible to assess global protein expression profiles in organisms with sequenced genomes. We implemented comprehensive proteomics to assess the expressed portion of the genome of Methylobacillus flagellatus during methylotrophic growth. We detected a total of 1,671 proteins (64% of the inferred proteome), including all the predicted essential proteins. Nonrandom patterns observed with the nondetectable proteins appeared to correspond to silent genomic islands, as inferred through functional profiling and genome localization. The protein contents in methylamine- and methanol-grown cells showed a significant overlap, confirming the commonality of methylotrophic metabolism downstream of the primary oxidation reactions. The new insights into methylotrophy include detection of proteins for the N-methylglutamate methylamine oxidation pathway that appears to be auxiliary and detection of two alternative enzymes for both the 6-phosphogluconate dehydrogenase reaction (GndA and GndB) and the formate dehydrogenase reaction (FDH1 and FDH4). Mutant analysis revealed that GndA and FDH4 are crucial for the organism's fitness, while GndB and FDH1 are auxiliary.

scholarly journals Identification of Proteins Differentially Expressed by Adipose-derived Mesenchymal Stem Cells Isolated from Immunodeficient Mice

2019 ◽  
Vol 20 (11) ◽  
pp. 2672 ◽  
Author(s):  
Yoshiki Nakashima ◽  
Saifun Nahar ◽  
Chika Miyagi-Shiohira ◽  
Takao Kinjo ◽  
Naoya Kobayashi ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Expression Profiles ◽  
Severe Combined Immunodeficiency ◽  
Therapeutic Effects ◽  
Immunodeficient Mice ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass ◽  
Protein Expression Profiles ◽  
And Function

Although cell therapy using adipose-derived mesenchymal stem cells (AdMSCs) regulates immunity, the degree to which cell quality and function are affected by differences in immunodeficiency of donors is unknown. We used liquid chromatography tandem-mass spectrometry (LC MS/MS) to identify the proteins expressed by mouse AdMSCs (mAsMSCs) isolated from normal (C57BL/6) mice and mice with severe combined immunodeficiency (SCID). The protein expression profiles of each strain were 98%–100% identical, indicating that the expression levels of major proteins potentially associated with the therapeutic effects of mAdMSCs were highly similar. Further, comparable levels of cell surface markers (CD44, CD90.2) were detected using flow cytometry or LC MS/MS. MYH9, ACTN1, CANX, GPI, TPM1, EPRS, ITGB1, ANXA3, CNN2, MAPK1, PSME2, CTPS1, OTUB1, PSMB6, HMGB1, RPS19, SEC61A1, CTNNB1, GLO1, RPL22, PSMA2, SYNCRIP, PRDX3, SAMHD1, TCAF2, MAPK3, RPS24, and MYO1E, which are associated with immunity, were expressed at higher levels by the SCID mAdMSCs compared with the C57BL/6 mAdMSCs. In contrast, ANXA9, PCBP2, LGALS3, PPP1R14B, and PSMA6, which are also associated with immunity, were more highly expressed by C57BL/6 mAdMSCs than SCID mAdMSCs. These findings implicate these two sets of proteins in the pathogenesis and maintenance of immunodeficiency.

P-652 Protein expression profiles in non-small cell lung cancer. A tissue microarray-based study of 142 cases

Lung Cancer ◽  
2005 ◽  
Vol 49 ◽  
pp. S290 ◽  
Author(s):  
E. Conde ◽  
R. García Luján ◽  
A. López Encuentra ◽  
L. Sánchez ◽  
M. Sánchez-Céspedes ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Protein Expression ◽  
Small Cell Lung Cancer ◽  
Tissue Microarray ◽  
Cell Lung Cancer ◽  
Expression Profiles ◽  
Small Cell ◽  
Small Cell Lung ◽  
Protein Expression Profiles

scholarly journals The nature of carbon dioxide substrate and equilibrium constant of the 6-phosphogluconate dehydrogenase reaction

1969 ◽  
Vol 115 (4) ◽  
pp. 633-638 ◽  
Author(s):  
R. H. Villet ◽  
K. Dalziel
Keyword(s):  
Carbon Dioxide ◽  
Free Energy ◽  
Equilibrium Constant ◽  
Heat Of Reaction ◽  
Phosphogluconate Dehydrogenase ◽  
Sheep Liver ◽  
Dehydrogenase Reaction ◽  
Reductive Carboxylation ◽  
Primary Substrate

1. It was shown that dissolved CO2 and not HCO3− or H2CO3 is the primary substrate for reductive carboxylation with 6-phosphogluconate dehydrogenase from sheep liver. 2. The equilibrium constant of the reaction was measured in solutions of various ionic strengths and at several temperatures, and the free energy and heat of reaction were determined.

scholarly journals Brain death induces the alteration of liver protein expression profiles in rabbits

2014 ◽  
Vol 34 (2) ◽  
pp. 578-584 ◽  
Author(s):  
BING DU ◽  
LING LI ◽  
ZHIBIAO ZHONG ◽  
XIAOLI FAN ◽  
BINGBING QIAO ◽  
...  
Keyword(s):  
Protein Expression ◽  
Brain Death ◽  
Expression Profiles ◽  
Liver Protein ◽  
Protein Expression Profiles

Fluoride exposure inhibits protein expression and enzyme activity in the lung-stage larvae ofAscaris suum

Parasitology ◽  
2006 ◽  
Vol 133 (4) ◽  
pp. 497-508 ◽  
Author(s):  
M. K. ISLAM ◽  
T. MIYOSHI ◽  
M. YAMADA ◽  
M. A. ALIM ◽  
X. HUANG ◽  
...  
Keyword(s):  
Protein Expression ◽  
Expression Profiles ◽  
Immunoblot Analysis ◽  
Specific Protein ◽  
Inorganic Pyrophosphatase ◽  
2D Electrophoresis ◽  
Peptide Mass ◽  
Enzyme Families ◽  
Protein Expression Profiles ◽  
Peptide Mass Spectrometry

Sodium fluoride (NaF) is an anion that has been previously shown to block the moulting process ofAscaris suumlarvae. This study describes moulting and development-specific protein expression profiles ofA. suumlung-stage L3 (AsLL3) following NaF exposure. AsLL3s cultured in the presence or absence of NaF were prepared for protein analysis using two-dimensional (2D) electrophoresis. NaF exposure inhibited at least 22 proteins in AsLL3 compared with moulted larvae (i.e. AsLL4). A further comparison of AsLL4 with those of pre-cultured AsLL3 and NaF-exposed AsLL3 revealed 8 stage-specifically and 4 over-expressed proteins. Immunoblot analysis revealed an inhibition by NaF of 19 immunoreactive proteins. Enzyme assay and immunochemical data showed an inhibition of the moulting-specific inorganic pyrophosphatase activity by 41% and a decreased expression in NaF-treated larvae, indicating its significance in the moulting process. A protein spot associated with NaF inhibition was isolated and identified by peptide mass spectrometry and bioinformatics approaches to be a member of 3–hydroxyacyl–CoA dehydrogenase/short-chain dehydrogenase enzyme families. These results have implications for the identification of proteins specific to the moulting process as potential chemotherapeutic targets.

ProteinChip Technology Reveals Distinctive Protein Expression Profiles in the Urine of Bladder Cancer Patients

2005 ◽  
Vol 47 (6) ◽  
pp. 885-894 ◽  
Author(s):  
J. Mueller ◽  
F. von Eggeling ◽  
D. Driesch ◽  
J. Schubert ◽  
C. Melle ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Protein Expression ◽  
Cancer Patients ◽  
Expression Profiles ◽  
Protein Expression Profiles

PATH-29. GLIOBLASTOMA TUMOR CLASSIFICATION BASED ON SPATIAL ANALYSIS OF ONCOGENIC AMPLIFICATIONS AND PROTEIN EXPRESSION

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi121-vi121
Author(s):  
Kacper Walentynowicz ◽  
Dalit Engelhardt ◽  
Shreya Yadav ◽  
Ugoma Onubogu ◽  
Roberto Salatino ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Protein Expression ◽  
Single Cell ◽  
Expression Profiles ◽  
Protein Profiling ◽  
Intratumor Heterogeneity ◽  
Neuronal Markers ◽  
Associated Proteins ◽  
Dual Amplification ◽  
Protein Expression Profiles

Abstract Heterogeneity of glioblastoma (GBM) has been extensively studied in recent years with identification of oncogenic drivers of GBM cellular subtypes. However, little is known about how these cells interact with each other or with the surrounding tumor microenvironment (TME). We employed spatial protein profiling targeting immune and neuronal markers (79 proteins) coupled with single-cell spatial maps of fluorescence in situ hybridization (FISH) for EGFR, CDK4, and PDGFRA on human GBM tissue sections. Several cores from 20 GBM samples were collected to create a tissue microarray, and 96 regions of interests were profiled with 37,844 nuclei for oncogenic amplification screen. Spatial protein profiling identified strong correlation of certain immune markers, TAU-associated proteins, and oligodendrocyte-enriched protein groups and overall high intratumor heterogeneity of TME. Our single-cell quantification of FISH signals showed differences among tumors based on the prevalence of dual amplification of EGFR and CDK4 within a cell relative to single oncogene amplified cells. High relative frequency of dual amplification was associated with increased expression of immune-related markers and decreased expression of EGFR protein. Moreover, this protein expression signature was associated with survival in another GBM dataset. Here, we present spatial genetic analysis at the single cell level coupled with protein expression profiles associated with tumor microenvironment. Our results suggest that assessment of genetic heterogeneity in GBM could potentially drive improved patient stratification and treatment.

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