An Attempt to Understand Kidney's Protein Handling Function by Comparing Plasma and Urine Proteomes

With the help of proteomics technology, the human plasma and urine proteomes, which closely represent the protein compositions of the input and output of the kidney, respectively, have been profiled in much greater detail by different research teams. Many datasets have been accumulated to form “reference profiles” of the plasma and urine proteomes. Comparing these two proteomes may help us understand the protein handling aspect of kidney function in a way, however, which has been unavailable until the recent advances in proteomics technology.After removing secreted proteins downstream of the kidney, 2611 proteins in plasma and 1522 in urine were identified with high confidence and compared based on available proteomic data to generate three subproteomes, the plasma-only subproteome, the plasma-and-urine subproteome, and the urine-only subproteome, and they correspond to three groups of proteins that are handled in three different ways by the kidney. The available experimental molecular weights of the proteins in the three subproteomes were collected and analyzed. Since the functions of the overrepresented proteins in the plasma-and-urine subproteome are probably the major functions that can be routinely regulated by excretion from the kidney in physiological conditions, Gene Ontology term enrichment in the plasma-and-urine subproteome versus the whole plasma proteome was analyzed. Protease activity, calcium and growth factor binding proteins, and coagulation and immune response-related proteins were found to be enriched.The comparison method described in this paper provides an illustration of a new approach for studying organ functions with a proteomics methodology. Because of its distinctive input (plasma) and output (urine), it is reasonable to predict that the kidney will be the first organ whose functions are further elucidated by proteomic methods in the near future. It can also be anticipated that there will be more applications for proteomics in organ function research

Urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells

Background Biomarkers are changes associated with the disease. Urine is not subject to homeostatic control and therefore accumulates very early changes, making it an ideal biomarker source. Usually, we have performed urinary biomarker studies involving at least thousands of tumor cells. However, no tumor starts from a thousand tumor cells. We therefore examined urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells. Methods Here, we serially diluted Walker-256 carcinosarcoma cells to a concentration of 102/mL and subcutaneously inoculated 0.1 mL of these cells into nine rats. The urine proteomes on days 0, 13 and 21 were analyzed by liquid chromatography coupled with tandem mass spectrometry. Results Hierarchical clustering analysis showed that the urine proteome of each sample at three time points were clustered into three clusters, indicating the good consistency of these nine rats when inoculated with the same limited tumor cells. Differential proteins on days 13 and 21 were mainly associated with cell adhesion, autophagic cell death, changes in extracellular matrix organization, angiogenesis, and the pentose phosphate pathway. All of these enriched functional processes were reported to contribute to tumor progression and could not be enriched through random allocation analysis. Conclusions Our results indicated that (1) the urine proteome reflects changes associated with cancer even with only approximately ten tumor cells in the body and that (2) the urine proteome reflects pathophysiological changes in the body with extremely high sensitivity and provides potential for a very early screening process of clinical patients

Dynamic Changes of Urine Proteome in Rat Models Inoculated with Two Different Hepatoma Cell Lines

Urine can accumulate systemic changes with no mechanism to be stable, which may reflect early changes associated with physiological or pathophysiological processes. To explore the potential value of the urine proteome, two rat models were established by intrahepatic injection of two different hepatoma cell lines, CBRH-7919 and RH-35. Urine samples were collected and analyzed. Compared with controls, the two models exhibited different numbers and types of differentially expressed urinary proteins despite having similar histological results. The results were compared with the urine proteome of a Walker 256 (W-256) liver tumor model. The differentially expressed urinary protein patterns in the three models were different. These findings demonstrate that changes in the urine proteomes of the two models can be detected at early stages and that the patterns of differentially expressed urinary proteins can differ even when the histological results are similar. Urinary proteins have potential utility for distinguishing among different tumor cells grown in the same organ

Changes to Urinary Proteome in High-Fat-Diet <i>ApoE</i>^−/− Mice

Cardiovascular disease is currently the leading cause of death worldwide. Atherosclerosis is an important pathological basis of cardiovascular disease, and its early diagnosis is of great significance. Urine bears no need nor mechanism to be stable, so it accumulates many small changes and is therefore a good source of biomarkers in the early stages of disease. In this study, ApoE-/- mice were fed a high-fat diet for 5 months. Urine samples from the experimental group and control group (C57BL/6 mice fed a normal diet) were collected at seven time points. Proteomic analysis was used for comparison within the experimental group and for comparison between the experimental group and the control group. The results of the comparison within the experimental group showed a significant difference in the urinary proteome before and after a one-week high-fat diet, and several of the differential proteins have been reported to be associated with atherosclerosis and/or as biomarker candidates. The results of the comparison between the experimental group and the control group indicated that the biological processes enriched by the GO analysis of the differential proteins correspond to the progression of atherosclerosis. The differences in chemical modifications of urinary proteins have also been reported to be associated with the disease. This study demonstrates that urinary proteomics has the potential to sensitively monitor changes in the body and provides the possibility of identifying early biomarkers of atherosclerosis

Nonlinear contact behavior of HTS tapes during pancake coiling and CORC cabling

Both the pancake coiling and conductor on round core (CORC) cabling processes consist of winding second-generation high-temperature superconducting tape (REBCO) in a core. The contact behavior between the tape and the core during the winding process directly affects the critical current, cable flexibility, mechanical support and electrical contact resistance. Therefore, the winding process needs to be optimized to produce pancake coils and CORC cables with the desired electrical and mechanical properties. This paper comprehensively considers the role of the relaxation and Poisson effects. The theoretical model and the finite element model (FEM) for calculating the contact stress during the winding process are established, and a formula for the estimation of the contact force is proposed. The suitable winding pre-tension force, winding curvature radius of SCS2030 (2 mm width and 30 µm substrate thickness) and SCS4050 (4 mm width and 50 µm substrate thickness) of REBCO tapes are obtained and discussed by accounting for the relaxation effect and the critical current degradation limit. With consideration of the Poisson effect, the nonlinear contact behavior is investigated. In addition, the relaxation effect, Poisson effect and plasticity of the REBCO tape are taken into account in the FEM model. The results show that the axial strain in the REBCO layer during the winding process is related to the contact behavior. The greater the winding pre-tension force, the smaller the helical curvature radius, and the greater the contact force. The distribution of contact stress for several winding factors (winding pre-tension force, winding angle and the core radius) is divided into three contact types: the single-line contact, the double-line contact and the surface contact. The FEM model results are consistent with the theoretical evaluation and are more suitable for practical winding cases. This research is the basis for designing and optimizing pancake coils and CORC cables

Online Extraction&ndash;DPPH&ndash;HPLC&ndash;DAD&ndash;QTOF-MS System for Efficient Screening and Identification of Antioxidants from Citrus aurantium L. var. amara (Rutaceae): Integrating Sample Preparation and Antioxidants Profiling

The lack of a direct connection between solid edible or medical natural products and bioactive compound profiling is a bottleneck in natural product research and quality control. Here, a novel integrated system, online extraction (OLE)&ndash;2,2&prime;-diphenyl-1-picrylhydrazyl (DPPH)&ndash;HPLC&minus;DAD&minus;QTOF-MS, was fabricated to extract, screen, and identify antioxidants from the whole fruit of Citrus aurantium L. var. amara (CAVA, Rutaceae) simply, rapidly, and efficiently. The system consumes less sample (1.0 mg of CAVA powder) and requires a shorter analytical time (45 min for sample extraction, antioxidants screening, separation, and identification). Eight antioxidant flavonoids were screened and identified, and six available flavanones were sensitively, precisely, and accurately quantified. Two major flavanone glycosides, naringin (50.37 &plusmn; 0.43 mg/g) and neohesperidin (38.20 &plusmn; 0.27 mg/g), exhibit potent DPPH scavenging activities with IC50 values of 111.9 &plusmn; 10.06 and 178.55 &plusmn; 11.28 &mu;g/mL. A minor flavanone aglycone, hesperitin (0.73 &plusmn; 0.06 mg/g), presents stronger DPPH scavenging activity (IC50, 39.07 &plusmn; 2.51 &mu;g/mL). Furthermore, density functional theory calculations demonstrated their electron transport ability and chemical reactivity, which confirmed the screened results. The results indicate that the developed OLE&ndash;DPPH&ndash;HPLC&minus;DAD&minus;QTOF-MS system provides new perspectives for analysis of antioxidants from complex natural products, which also contribute to the quality evaluation of CAVA

A comparison of E15.5 fetus and newborn rat serum proteomes

<p>Abstract</p> <p>Background</p> <p>Serum proteins carry out several functions in the circulation, including transfer, immunological functions, messenger functions, coagulation, and regulation of homeostasis. To investigate changes in serum proteins that occur during development, the serum proteomes of embryonic 15.5 (E15.5) fetuses and newborn rats were compared using LC-MS/MS.</p> <p>Results</p> <p>A total of 958 proteins were identified in the serum of rats at both developmental stages. The serum proteome pattern of newborn rats was compared to E15.5 fetuses by relative quantitation. The expression patterns of hemoglobin subunits were different at the two stages, with most of the subunits having decreased expression in newborn rats compared to E15.5 fetuses. In addition, 8 of 12 apolipoproteins were significantly decreased and 10 of 11 identified complement molecules were increased, with 4 exhibiting a significant increase. Moreover, 11 of 14 of the significantly increased enzyme regulators were inhibitors. The serum proteome patterns of different littermates from both developmental stages were also compared. We found that the levels of many highly abundant serum proteins varied between littermates, and the variations were larger than the variations of the technical control.</p> <p>Conclusions</p> <p>The serum proteomes of newborn rats and E15.5 fetuses were compared. The expression patterns of hemoglobin subunits were different at the two developmental stages, with most of the subunits having decreased expression. The majority of apolipoproteins had significantly decreased expression, while almost all identified complement proteins had increased expression. The levels of several highly abundant serum proteins also varied among littermates at these two developmental stages. This is the first study using LC-MS/MS to investigate serum proteome development.</p

Table_7_Changes in the urinary proteome before and after quadrivalent influenza vaccine and COVID-19 vaccination.xlsx

The proteome of urine samples from quadrivalent influenza vaccine cohort were analyzed with self-contrasted method. Significantly changed urine protein at 24 hours after vaccination was enriched in immune-related pathways, although each person’s specific pathways varied. We speculate that this may be because different people have different immunological backgrounds associated with influenza. Then, urine samples were collected from several uninfected SARS-CoV-2 young people before and after the first, second, and third doses of the COVID-19 vaccine. The differential proteins compared between after the second dose (24h) and before the second dose were enriched in pathways involving in multicellular organismal process, regulated exocytosis and immune-related pathways, indicating no first exposure to antigen. Surprisingly, the pathways enriched by the differential urinary protein before and after the first dose were similar to those before and after the second dose. It is inferred that although the volunteers were not infected with SARS-CoV-2, they might have been exposed to other coimmunogenic coronaviruses. Two to four hours after the third vaccination, the differentially expressed protein were also enriched in multicellular organismal process, regulated exocytosis and immune-related pathways, indicating that the immune response has been triggered in a short time after vaccination. Multicellular organismal process and regulated exocytosis after vaccination may be a new indicator to evaluate the immune effect of vaccines. Urinary proteome is a terrific window to monitor the changes in human immune function.</p