Can proteomics elucidate mechanisms of antimicrobial resistance in Neisseria gonorrhoeae that whole genome sequencing is unable to identify? An analysis of protein expression within the 2016 WHO N. gonorrhoeae reference strains

2019 ◽  
Vol 96 (5) ◽  
pp. 330-334 ◽  
Author(s):  
Jianhe Peng ◽  
Julie Russell ◽  
Sarah Alexander
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Protein Expression ◽  
Stress Responses ◽  
Atp Hydrolysis ◽  
Efflux Pump ◽  
Expression Profiles ◽  
Internal Standard ◽  
Protein Expression Profiles ◽  
Reference Strains

ObjectivesAntimicrobial resistance (AMR) in Neisseria gonorrhoeae is of increasing concern. This study established a quantitative, scalable proteomics method to examine the WHO panel of N. gonorrhoeae isolates with completed closed genomic sequences and well-defined phenotypical and genotypical AMR patterns, to gain a greater understanding of AMR in N. gonorrhoeae.Methods14 WHO reference strains were propagated, pooled stable isotope labelled lysates were used as an internal standard (IS). Protein lysates were mixed with IS, digested with trypsin and fractionated before analysis by nano-LC/MS/MS, in triplicate. The susceptible strain WHO F was used as reference to which the proteomic profiles of other strains were compared. Hierarchical clustering and permutation adjusted t-tests were performed to find proteins with significant fold changes.ResultsStandardised, reproducible protein expression profiles in N. gonorrhoeae reference strains were produced. Strains that have previously been shown to be highly similar using genomics, displayed different proteomic profiles. Several proteins from efflux pumps to stress responses, such as oxidative stress, toxin/antitoxin systems, were found to be altered in AMR strains. LtgE was upregulated in strains which displayed chromosomally mediated resistance to penicillin. MacB (the ATP hydrolysis part of macrolide efflux pump MacA-B), was ~twofold upregulated in WHO V (MIC of azithromycin >256 mg/L) and maybe associated with azithromycin resistance.ConclusionsA robust method was developed to study protein expression in N. gonorrhoeae. The proteome profiles could differentiate genetically similar stains. This study identified complex mechanisms in N. gonorrhoeae which may be associated with AMR.

Changes in Metabolite and Protein Expression Profiles of Atypical Dark-cutting and Normal-pH Beef

2021 ◽  
Vol 99 (Supplement_2) ◽  
pp. 16-16
Author(s):  
Frank Kiyimba ◽  
Steven Hartson ◽  
Janet Rogers ◽  
Gretchen G Mafi ◽  
Ranjith Ramanathan
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Protein Expression ◽  
Stress Responses ◽  
Expression Profiles ◽  
Mass Spectrometry Analysis ◽  
Network Analyses ◽  
Coa Transferase ◽  
Muscle Ph ◽  
Protein Expression Profiles

Abstract The color of meat is an important deciding factor in consumers’ assessment of meat quality. To meat buyers, the bright cherry-red color of meat indicates freshness and wholesomeness. However, atypical dark-cutting beef represents dark-colored meat with a muscle pH between 5.6 and 5.8. Although previous studies have indicated that the ultimate pH of atypical dark-cutting beef is greater than normal, the mechanistic basis for the occurrence is not clear. Therefore, the objective of this study was to identify protein and metabolite profiles of normal and atypical dark-cutting beef. Longissimus thoracic (LT) muscles from 12 different animals (6 atypical dark-cutters and 6 normal-pH beef) were analyzed by comparing changes in metabolites and protein profiles using GC-MS non-targeted metabolomics and LC-MS/MS-based proteomics, respectively. Metabolomics analysis showed down-regulation of glycolytic metabolites such as glucose-6-phosphate, lactose, and glucose, indicating a reduced capacity to accumulate lactate postmortem in atypical dark-cutters compared with normal-pH beef. Mass spectrometry analysis identified 66 proteins with significant changes in protein expression profiles (P < 0.05) between atypical and normal-pH beef. Of these, 22 proteins were up-regulated while 14 were down-regulated in atypical dark-cutting beef. Functional annotation and protein-protein interaction network analyses revealed that up-regulated proteins such as NADH ubiquinone oxidoreductase subunit A7, ATPase Na+/K+ transporting subunit alpha 2, 3-oxoacid CoA-transferase 1, cytochrome b5 reductase 3, actinin alpha 4, tropomyosin 2, heat shock protein beta-7, and DnaJ heat shock protein family (Hsp40) member B4 are involved in energy synthesis, muscle contraction and stress responses. By contrast, down-regulated proteins, including phosphofructokinase, glycogen phosphorylase, amylo-alpha-1,6-glucosidase, phosphorylase kinase regulatory subunit alpha and gamma are involved in glycogen metabolism. In summary, lower glycolytic metabolites and glycogen degradation enzymes are associated with differences in muscle pH and color of atypical dark-cutting beef.

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 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.

Upregulation of PKC genes and isozymes in cardiovascular tissues during early stages of experimental diabetes

2003 ◽  
Vol 12 (2) ◽  
pp. 139-146 ◽  
Author(s):  
Mingzhang Guo ◽  
Mack H. Wu ◽  
Ferenc Korompai ◽  
Sarah Y. Yuan
Keyword(s):  
Protein Expression ◽  
Cardiovascular System ◽  
Time Course ◽  
Experimental Diabetes ◽  
Pathological Condition ◽  
Expression Profiles ◽  
Diabetic Patients ◽  
Mrna Levels ◽  
Early Stages ◽  
Protein Expression Profiles

The protein kinase C (PKC) pathway has recently been recognized as an important mechanism in the development of diabetic complications including cardiomyopathy and angiopathy. Although an increase in PKC kinase activity has been detected in the cardiovascular system of diabetic patients and animals, it is unclear whether the same pathological condition alters PKC at the transcriptional and translational levels. In this study we assessed quantitatively the mRNA and protein expression profiles of PKC isozymes in the heart and vascular tissues from streptozotocin-induced diabetic pigs. Partial regions of the porcine PKCα, β1, and β2 mRNAs were sequenced, and real-time RT-PCR assays were developed for PKC mRNA quantification. The results showed a significant increase in the mRNA levels of PKCα, β1, and β2 in the heart at 4–8 wk of diabetes. In concomitance, the PKCβ1 and β2 genes, but not the PKCα gene, were upregulated in the diabetic aorta. Correspondingly, there was a significant increase in the protein expression of PKCα and β2 in the heart and PKCβ2 in the aorta with a time course correlated to that of mRNA expression. In summary, PKCβ2 was significantly upregulated in the heart and aorta at both the transcriptional and translational levels during early stages of experimental diabetes, suggesting that PKCβ2 may be a prominent target of diabetic injury in the cardiovascular system.

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