Comparison of urine proteome in rats intraperitoneally infected by different microorganisms / 生物工程学报

Different microorganisms can cause intraperitoneal infection. This study was to distinguish different microbial infections by urine analysis. Rats were intraperitoneally injected with Escherichia coli, Staphylococcus aureus, and Candida albicans, separately. Urine samples were collected from rats at 0, 12, 36 and 72 h after infection. Urinary proteins were profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with the control (without infection), a total of 69 differential proteins were identified in rats injected with E. coli. A total of 31 differences proteins were identified in rats injected with S. aureus. A total of 38 differential proteins were identified in rats injected with C. albicans. Urine proteome was different when rats were infected by different microorganisms, suggesting that urine may have the potential for differential diagnosis of different intraperitoneal infections.

Comparison of urinary proteomes among rats, guinea pigs and golden hamsters / 生物工程学报

Biomarkers are the detectable changes associated with physiological or pathological changes. Urine as excreta of the body, without the mechanisms to maintain a homeostatic internal environment, can reflect a variety of changes in the body. Using animal models can simulate human disease processes, monitor disease changes, and provide clues to early diagnosis. Rats as commonly used model animals are not the dominant models for all disease, thus comparing the urinary proteins of rats with other animals to provide clues to the selection of other animal dominant models. In this study, urinary proteins were digested and profiled by liquid chromatography and tandem mass spectrometry (LC-MS/MS). The urinary proteins of rats, guinea pigs and golden hamsters were compared. The results showed that the number of urine proteins in the three different animals was different, and also different in every system of the body. This provides a basis for selecting the best animal models for different diseases.

Changes of urinary proteins in a bacterial meningitis rat model / 生物工程学报

Unlike cerebrospinal fluid or blood, urine accumulates metabolic changes of the body and has the potential to be a promising source of early biomarkers discovery. Bacterial meningitis is a major cause of illness among neonates and children worldwide. In this study, we used Escherichia coli-injected rat model to mimic meningitis and collected urine samples on day 1 and day 3. We used two different methods to digest proteins and analyzed peptides by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We identified 17 and 20 differential proteins by two methods respectively on day 1, and 5 differential proteins by filter-aided digestion method on day 3. Finding these differential proteins laid a foundation to further explore biomarkers of bacterial meningitis.

Elution of urinary proteins preserved on nitrocellulose membrane with heating / 生物工程学报

The preservation of urinary proteins on a membrane plays a vital role in biomarker research, and the efficient elution of proteins preserved on nitrocellulose membrane (NC membrane) determines the application of this method. During the heating elution procedure, we raised the temperature to reduce the intense vortexing time, and kept gentle rotating while precipitation to prevent nitrocellulose reformation. We also used SDS-PAGE and LC-MS/MS to analyze the urinary proteins prepared by heating elution procedure, intense vortexing elution procedure and acetone precipitation method. There was no degradation of proteins prepared by heating elution procedure. Compared with proteins prepared by heating elution method and acetone precipitation method, the overlapping rates of the proteins was almost the same (92.6% versus 96.8%) and the ratios of CV values (< 20%) of the proteins were both high (85.2% and 94.4%). The heating elution procedure achieved good technical reproducibility, and was much simpler and more efficient than the previous one. It can facilitate the application of the preservation of urinary proteins on membrane.

Comparison of two urinary protein preparation methods: nitrocellulose membrane preservation and acetone precipitation / 生物工程学报

Nitrocellulose membrane based urinary protein preservation method is simple, fast and economic, but its advantage over the traditionally used acetone precipitation method is still unclear. In this work, we prepared urinary proteins by the two methods by LC-MS/MS. Then we used protein spectra counts to assess the reproducibility of the two methods. Proteins identified by the two methods were almost the same in number, spectral count distribution and distribution of coefficients of variation value. In conclusion, nitrocellulose membrane method is generally the same as acetone precipitation method. It can be used for large scale preservation of clinical urine samples.

Preface for special issue on proteomics (2014) / 生物工程学报

Proteomics is one of the most important functional genomics research in the post-genomic era, which is closely related to medical biology, chemistry, physics, information science and modern technology. Through review research progress of some important proteomics, a proteomics special issue is published so as to find problems, explore the possible applications and outlook the development prospects of proteomics. The special issue consists of reviews and original papers, mainly involving in the following aspects, i) proteomics about different species such as humans, mammals, prokaryotes and actinobacterial; ii) proteomics methodology and techniques including tandem mass spectrometry analysis, film (urimem) preservation of urine protein, quantitative proteomic analysis and meta analysis; iii) function and application of proteome such as spider (Latrodectus tredecimguttatus) toxins proteome, protein phosphorylation proteome, oocytes and early embryos proteomes, liver fibrosis proteome, drug-resistant mycobacterium tuberculosis proteome, etc.

Comparison of cost-effectiveness between Urimem and direct freezing for urinary protein preservation / 生物工程学报

To compare two enrichment and preservation methods of urinary proteins, stored in polyvinylidene difluoride (PVDF) membrane (Urimem) or direct freezing, we examined the differences between the two methods in time, space, costs of supplies and electricity, degree of protein degradation and convenience of the sample handling. The urimem method is superior in the storage space, the cost of electricity and the clinical convenience compared to the direct freezing method. However, the direct freezing method is superior in the time and the cost of supplies to the urimem method. The enrichment and preservation of urinary proteins using urimem have more cost-effective benefits compared to those of the direct freezing method.

Establishment of urinary proteome and functional analysis of urinary differential proteins in patients with metabolic syndrome / 中华临床营养杂志

ObjectiveTo establish the urinary proteome profile of the metabolic syndrome ( MetS ) patients,compare the different urinary proteins between the MetS patients and the normal individuals,and analyze the function of the different proteins,so as to explore the pathogenesis of MetS.MethodsOvernight urine were collected from normal controls (n =6) and MetS patients ( n =6).Acetone precipitation method was used to precipitate proteins of urine.Intra-group proteins were mixed together,identified by reversed phase liquid chromatography-mass spectrometry/mass spectrometry and quantified relatively using spectral counting method.The functions of differential proteins were analyzed using Panther.ResultsA total of 807 and 630 proteins were identified respectively in normal controls and MetS patients.Comparing MetS patients with normal controls,sixty different proteins were found,of which 23 proteins were up-regulated and 37 proteins were down-regulated in MetS patients.In the up-regulated proteins,plasminogen was involved in the plasminogen activation cascade and isoform of alphaenolase,phosphoglycerate kinase 1 and fructose-bisphosphate aldolase B down-regulated in MetS patients were involved in the process of glycolysis and fructose metabolism.ConclusionsThe urinary proteome profile of patients with MetS was established by reversed phase liquid chromatography-mass spectrometry/mass spectrometry.Different proteins between MetS patients and normal people were identified.The plasminogen activation cascade,glycolysis and fructose metabolism play key roles in the pathogenesis of MetS.

Analysis of differential urinary proteome in experimental minimal change nephropathy / 基础医学与临床

Objective To screen early urine protein markers for minimal change nephropathy.Methods Adriamycin nephropathy was employed as minimal change nephropathy model.Urinary protein and ConA captured glycoproteins were respectively profiled.Results By profiling urine proteome,25 differential proteins were identified.These differential proteins were from leaked plasma proteins,secreted proteins from immuno-and inflammatory cells,specifically asecreted proteins from urinary tract,and so on.They took part in different pathogenic process,eg.hemodynamic changes,podocytes injury,immunological disorder and so on.By profiling ConA-enriched urinary glycoproteome,21 differential proteins were identified,among which 12(57%) were different from the above 25 differential proteins.This indicates that the knowledge of urine glycoproteome is complementary to urine proteome in understanding kidney condition.Conclusion These differential proteins can be potential indicators of minimal change nephropathy,and can help better understand the pathogenesis by further studying their functions.

Characterization of ligand-binding properties of PDZ domain of Veli3 by screening random peptide library / 基础医学与临床

Objective To investigate the ligand-binging characteristics of Veli3 PDZ.Methods Random peptide library was screened using yeast two-hybrid method with Veli3 PDZ as bait.In combination with bioinformatics method all the potential ligands in human proteome were predicted by searching human databases with the consensus-binding sequences.Fourteen native human proteins predicted as ligands were chosen by their cellular locations and biological functions for validating protein interaction in yeast two-hybrid system.Results The C-terminal consensus sequences for the Veil3 PDZ binding is X-COOH(X denotes any amino acid),which indicates that Veli3 PDZ belongs to classⅠ.Six of fourteen native human proteins predicted as ligands were confirmed to be positive in the yeast two-hybrid system.There were a lot of interactions between PSD-95,another PDZ protein,and the ligands of Veli3 PDZ reported previously and discovered in this study.Conclusion The six novel potential ligands of Veli3 found in this study provide significant clues for discovering biological functions of Veil3 proteins.Moreover,Veli3 PDZ and PSD-95 PDZ may compete in binding the same ligands.

Strengthen the scientific quality of graduate students by literature presentation and discussion course / 基础医学与临床

The main objective of today’s graduate education reform is to improve the quality of graduate students. Curriculum development, as an essential part of graduate education, is pivotal to this goal. While classroom teaching innovation is placed in the front of curriculum development, it has become an important issue for graduate education study to practice an alternative capability centered way other than the current knowledge centered classroom teaching. We offered the course called "literature presentation and discussion" to the class 2006 graduate students at Chinese Academy of Medical Sciences. This article briefed and discussed the purpose,practice of this course,feedbacks from students and problems and solutions.

Progress in glycoproteome research / 基础医学与临床

As one of the important areas in proteomics,glycoproteome is in the spotlight currently.In this paper,the description of glycoproteins,the enrichment methods of glycoproteins/glycopeptides,the identification approaches of glycoproteins/glycopeptides and the application of glycoproteome were overviewed.

Construction of a non-redundant human SH2 domain database / 基因组蛋白质组与生物信息学报·英文版

Domain database is essential for domain property research. Eliminating redundant information in database query is very important for database quality. Here we report the manual construction of a non-redundant human SH2 domain database. There are 119 human SH2 domains in 110 SH2-containing proteins. Human SH2s were aligned with ClustalX, and a homologous tree was generated. In this tree, proteins with similar known function were classified into the same group. Some proteins in the same group have been reported to have similar binding motifs experimentally. The tree might provide clues about possible functions of hypothetical proteins for further experimental verification.