To separate the overlapped protein spots in two-dimensional gel electrophoresis (2-DE) images, we proposed an auto-separating algorithm based on valley characteristics. Firstly, the marker-controlled watershed algorithm was used to detect the initial outlines of the object regions. Secondly, medial axis transform and hierarchical branch pruning method were applied to the main skeletons of the object regions, and each main skeleton was fitted into line segments to describe the overlap directions. Then, the 3-dimensional model of the object region was scanned on the normal planes of the line segments to find the valley locations. And finally, a validation model was adopted to construct separation lines. The experiments on 2 real scanned 2-DE images showed that the true overlap separate (TOSs) were 78.95% and 85.71%, respectively. The results indicated that the proposed algorithm was better than the existing algorithms and could be used in engineering practice.
Algorithms ; Electrophoresis, Gel, Two-Dimensional ; Proteins ; chemistry

Electrophoresis, Gel, Two-Dimensional ; methods ; Humans ; Proteomics ; methods ; Urinalysis ; methods

Proteomics and polemic techniques are among the most valuable approaches in the research of life science in this new century, marking the beginning of a post-genome era. Two-dimensional electrophoresis and mass spectrometry, applied as key techniques in proteomic research, have given rise to new research strategies and improved the efficiency of researchers in exploring the unknown field. Its introduction into the exploration of spermatozoal proteins has given us so many pleasant surprises. This review presents some essential information about proteomics and two-dimensional electrophoresis and mass spectrometry, with a brief introduction of the recent progress in the researches on human sperm proteome, capacitation-related sperm proteins, sperm-egg interaction-related proteins, and sperm-immunity which has made great senses in the clinical problems.
Electrophoresis, Gel, Two-Dimensional ; Humans ; Male ; Proteome ; Spermatozoa ; immunology

Aims: Acinetobacter baumannii has been identified as one of the six most pathogenic bacteria that is the cause of most hospital bacterial infections according to Infectious Disease Society of America (IDSA). These nosocomial pathogens are notorious worldwide due to its ability in causing lethal infections among immunocompromised patients and its resistance to many strong antibiotics. This study aims to compare the expressed proteins of two A. baumannii strain, ATCC 19606 and a pathogenic clinically isolated strain known as AB-13. Methodology and results: AB-13 clinically strain was isolated from the lower respiratory tract of a patient with pneumonia. In this study, the proteomic profile of both ATCC 19606 and AB-13 are produced using 2-dimensional gel electrophoresis. The total protein contents were extracted, quantified and separated using 2-DE with a pH range of 4-7 to acquire the proteomic profile for comparison. The final analytical gel was analysed using Delta2D software and among the 324 protein spots successfully resolved, 10 spots exhibited signs of differential expression with 7 spots found to be downregulated and 3 spots upregulated (p< 0.01). These differences could signify the evolution AB-13 has undergone as it acquires traits ultimately aiding in its survivability, antimicrobial resistance and pathogenicity within varied environments especially during infections. Conclusion, significance and impact of study These findings support the presence of variation in AB-13 from a proteomic perspective, highlighting the pathogen’s evolution improving survivability and pathogenicity, warranting in-depth exploration towards understanding A. baumannii virulence and pathogenicity.
Acinetobacter baumannii--pathogenicity ; Two-Dimensional Difference Gel Electrophoresis ; Proteomics

We investigated the biochemiesl change of keratin by the methods of SDS-PAGE and Two-dimensional gel electrophoresis, and observed electron microscopic ultrestructural changes in five Unna-Thost palmoplantar keratoderma patients and two normal adults. The results are summarized as follows : 1. The increased bands of 51 kd and newly appearing 48 kd, 56 kd keratins were observed on the SDS-PAGE and compared to the normsl control. 2. The newly appearing 48 kd(acidic) paired with 56 kd(basic) keratins and 51 kd keratin and the disappearance of 59 kd(basic), 64 kd(basic) keratins were observed on the two-dimensional gel electrophoresis and compared to the normal control. 3. The variable sized, numerous, globular, irregularly beam-shaped and granular kerstohyaline granules were scattered in the granular cell and corneocyte. Numerous ribosomes were noted between the clumped tonofibrils and around the keratohyaline granules. The lipid droplets were seen in the corneocytes and granular cells on the electron microscope.
Adult ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Humans ; Keratoderma, Palmoplantar* ; Ribosomes

In this study,the protein in different Cordyceps samples,which include fresh sample( S1),22 ℃ drying sample( S2),37 ℃ drying sample( S3) and 60 ℃ drying sample( S4),were analyzed by sodium dodecylsupinate-polyacrylamide gel electrophoresis( SDS-PAGE) and two-dimensional electrophoresis( 2-DE). The total protein contents in Cordyceps samples were from 1. 655-4. 493 mg·g~(-1) and the protein contents in fresh sample was the highest. The results of SDS-PAGE showed that the mainly ranges of protein molecular weight of Cordyces samples were 10-100 kDa and the numbers of protein bands were 28 to 41,the fresh sample had the maximum number of protein bands. The 2-DE profiles were analyzed by PDQuest software. The resulted indicated that 488-876 protein spots were detected in different Cordyceps samples and the isoelectric point( pI) was distributed between 4. 5 and 6. 5,the protein molecular weight was distributed in 10-20 kDa and 25-100 kDa,the fresh sample had the maximum number of protein spots. Therefore,the drying process could decrease contents and species of protein in Cordyceps,and the different drying conditions had different effects on protein. These results provide a reference for improving the drying process of Cordyceps.
Cordyceps ; chemistry ; Desiccation ; methods ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Fungal Proteins ; analysis ; Molecular Weight

The biological interpretation of two-dimensional (2D) gel electrophoresis experiments is a key step toward understanding the functions of biological systems. We here present a web-based integrated database, called 2DSpotDB, for the management of proteome data derived from several pathogens. The 2DSpotDB was established as a part of the management of a pathogen proteome project at the Korea National Institute of Health. The goals of the 2DSpotDB implementation are to store and define important pathogen genes, retrieve information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry, and create an integrated system to provide pathogen proteome information for biological scientists. This database currently contains 14 gels and information on 387 protein spots, among which 329 proteins were identified and annotated.
Acrylic Resins ; Data Mining ; Electrophoresis ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Gels ; Korea ; Mass Spectrometry ; Proteins ; Proteome

BACKGROUND: To investigate the molecular basis for invasion of malignant gliomas, proteomic analysis approach was carried out using two human glioma cell lines, U87MG and U343MG-A that demonstrate different motility and invasiveness in in vitro experiments. METHODS: High-resolution two-dimensional gel electrophoresis and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry analysis were performed. RESULTS: Nine distinct protein spots that were recognized with significant alteration between the two cell lines. Five of these protein spots were up-regulated in U87MG and four were up-regulated in U343MG-A. CONCLUSION: Among these proteins, cathepsin D was shown to be one of the important proteins which are related with glioma invasion. However, further studies are necessary to reveal the exact role and mechanism of cathepsin D in glioma invasion.
Cathepsin D ; Cell Line* ; Electrophoresis, Gel, Two-Dimensional ; Glioma* ; Humans ; Mass Spectrometry ; Proteomics

OBJECTIVETo study the differences of protein expression levels in the brain cortex of human fetus and adult with proteomics technique, and provide preliminary data on the change of proteins during brain development.

METHODSProteins extracted from human temporal lobes in fetal (3 month and 5 month respectively) and adult (30 years old) brain were separated by two-dimensional gel electrophoresis (2DE). The proteins were then stained with colloidal Coomassie blue to produce a high-resolution map of the proteiome. The differential protein spots were analyzed by PDQuest 7.0 software and 8 spots, which were gradually reduced or gradually increased in brain development process and the protein spots of difference over two-fold in the brain, were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF/TOF).

RESULTS(1) On average, 642, 511 and 527 protein spots could be obtained in the temporal lobes of adult, 3 month and 5 month fetus. The matching rate of images was 87%. The basic proteins in adult brain were obviously much more than that in the fetus; (2) There were 172, 171 and 152 singular protein spots in temporal lobes of adult, 3 month and 5 month fetus respectively.(3) Compared with adult, there were 131 and 115 different protein spots in the 3 month and 5 month fetus respectively. There were 60 and 40 protein spots with more than 2 fold difference, among which 24 and 17 were down-regulated, and 36 and 23 were up-regulated respectively. (4) There was different expression in proteins such as serum albumin, triosephosphate isomerase, etc. in the 3 groups. Fatty acid binding protein 7 and unnamed proteins were only highly expressed in the 3 month brain; ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit and transducin beta-1 subunit were up-regulated in adult brain. Serum albumin decreases gradually with brain development. However, ATP synthase, mitochondrial F0 complex, and triosephosphate isomerase increase gradually with brain development.

CONCLUSIONThe proteins of human brain cortex were obviously changed from embryonic stage to adult. The differentially displayed proteins may provide further insight into the understanding of development of human brain.

Adult ; Cerebral Cortex ; metabolism ; Electrophoresis, Gel, Two-Dimensional ; Fetus ; metabolism ; Humans ; Mass Spectrometry ; Proteins ; metabolism ; Proteomics

OBJECTIVETo optimize a pretreatment method of urine proteomics in children with primary nephrotic syndrome.

METHODSUrine from children with primary nephrotic syndrome was treated in different pH and isolated by cold acetone precipitation for different durations. Then the amounts and kinds of proteins were compared by quantify, SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE) in order to optimize a way to deal with urine protein.

RESULTSMost proteins were obtained at pH 2.7. The amounts of protein precipitated by acetone for 0.5 hr was obviously less than those precipitated for 1 and 2 hrs (P<0.05), while there was no significant difference between the amount of protein precipitated for 1 and for 2 hrs. Protein precipitated by cold acetone for 1 hr at pH 2.7 was selected as the best pretreatment method. Satisfactory 2-DE maps can be acquired.

CONCLUSIONSUrine protein can be best obtained at pH 2.7 and precipitated by cold acetone for 1 hr.

Child ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Hydrogen-Ion Concentration ; Nephrotic Syndrome ; urine ; Proteinuria ; urine ; Proteomics ; methods