Conformer Analysis of a Biological G-Quadruplex Element in the Human c-MYC Promoter by Native Polyacrylamide Gel Electrophoresis

The G-quadruplexes undergo complex folding and conformation exchanges.G-quadruplex stability is substantially influenced by sequence,bufer and temperature.Mutational analysis together with nuclear magnetic resonance spectroscopy(NMR),X-ray crystallography and circular dichroism spectroscopy has been proved to be a powerful approach for G-quadruplex structural analysis.Herein,we used DNA sequence mutation and native polyacrylamide gel electrophoresis to investigate the topology and conformations of a G-quadruplex model molecule Pu18 found in the human c-MYC promoter.The guanines(G6,G9 or G18)which were not contributable to G-tetrad formation in c-MYC Pu18 sequence were mutated to thymine or adenine.We screened the buffer and temperature of gel electrophoresis for Pu18.Gel electrophoresis showed that two of the four conformers of c-MYC Pu18 in 100 mM K+buffer were resolved,which was in accordance with the conformations as determined by the 1 H NMR spectra in previous studies.This technique is expected as a general methodology for its easy operation and low cost to facilitate uncovering more yet unidentified G-quadruplex folds and functions,with the assistance of other analytical methods like NMR,X-ray crystallography and circular dichroism spectroscopy.

Characterization of Agro-diversity by Seed Storage Protein Electrophoresis:Focus on Rice Germplasm from Uttarakhand Himalaya,India

The characteristics of 48 rice varieties from Uttarakhand Himalaya, India were detected by morphological and biochemical markers. The grains of the selected rice varieties varied in their morphological （grain length, grain width and grain weight） and biochemical characters （sodium dodecyl sulfate polyacrylamide gel electrophoresis, SDS-PAGE）. Based on the presence of 70, 65, 60, 57, 37-39, 22-23, 13 and 10 kDa protein bands in the 48 rice varieties, seven types of profiles were identified. An unweighted pair group average method with arithmetic mean （UPGMA） dendrogram based on cluster analysis of genetic similarity of the protein bands showed two distinct groups with 1%-78% similarity coefficients. The presence of characteristic bands in selected varieties is a useful parameter for identification of rice germplasm.

Non-decoloured In-gel Digestion of Coomassie Blue-stained Proteins

A simplified method is presented for tryptic digestion of Coomassie brilliant blue(CBB)-stained proteins in polyacrylamide gels. Compared with conventional methods, the proposed method does not require a removal of the dye before digestion, and is thus faster and saves a lot of labor. The resulted digest can be analyzed by either RPLC/ESIMS or MALDI MS for identification of the protein in a conventional way. Model studies with bovine serum albumin(BSA) showed that 50 ng of the protein could be routinely identified. The simplified procedure displays a tendency to produce more incompletely cleaved peptides, which is favorable for improving the sequence coverage.

Diagnosis of disease-specific proteins in cerebrospinal fluid of children infected with tuberculous meningitis

BACKGROUND： Isolated mycobacterium tuberculosis from cerebrospinal fluid （CSF） is regarded as the ＂gold standard＂ for diagnosis of tuberculous meningitis （TBM）. However, culture of CSF specimens is time-consuming and lacks sensitivity. There is a strong need to determine complementary disease-specific markers, which are essential for increasing early diagnosis and improving prognosis in patients with TBM OBJECTIVE： To establish proteomic profiles of CSF in TBM and normal children using two-dimensional polyacrylamide gel electrophoresis, and to screen for disease-specific proteins. DESIGN, TIME AND SETTING： The case-control study was conducted at the Department of Pediatrics, Xiangya Hospital of Central South University and the Key Laboratory of Cancer Proteomics of Ministry of Public Health of China between January 2008 and January 2009. PARTICIPANTS： The TBM group included three patients with a strongly positive tuberculin skin test, as well as positive CSF mycobacterial staining and culture, who were admitted to the Department of Pediatrics, Xiangya Hospital from January 2008 to January 2009. Three healthy, age- and gender-matched children served as the control group. METHODS： CSF proteins were separated using two-dimensional polyacrylamide gel electrophoresis in both groups. Gels were scanned using Image scanner and LabScan software. Differentially expressed proteins were analyzed using PDQuest 7.0 software. The clearly discernible spots, which were expressed only in the TBM group, were chosen to perform matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. MAIN OUTCOME MEASURES： Differentially expressed spots on CSF profiles of TBM and normal children were measured. RESULTS： Following comparison of two-dimensional polyacrylamide gel electrophoresis maps between TBM and control groups, 546 and 533 spots were detected, respectively. A total of 64 differentially expressed proteins were observed between the groups, including 15 upregulated spots, eight downregulated spots, 27 spots that were exclusively expressed in the TBM group, and 14 spots that were exclusively expressed in the control group. At total of 20 spots that were exclusively expressed in the TBM group were chosen for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis, and 20 peptide mass fingerprints were obtained. After searching the data base, 16 proteins were matched. CONCLUSION： Two-dimensional polyacrylamide gel electrophoresis profiles of the CSF proteome were successfully established in the TBM and normal children. Parts of these differentially expressed proteins were identified through mass spectrometry and bioinformatics. Results indicated that apolipoprotein A I, anti-tumor necrosis factor-alpha antibody, crystal structure of MRP14 and HLA class II histocompatibility antigen DRB1-4 could be closely correlated with TBM pathogenesis.

Quasispecies groups in the core promoter region of hepatitis B virus

Objectives: To investigate the mutation of the basic core promoter (BCP) of hepatitis B virus (HBV) and clarify the significance of HBV quasispecies groups in patients with chronic HBV infection. Methods: A set of specific primers was synthesized according to the HBV DNA sequence of a Chinese strain. The BCP was amplified by PCR method from the serum of 40 patients with chronic HBV infection, and the PCR products of 2 patients were subcloned into pGEM Teasy vectors. Polyacrylamide gel elec- trophoresis (PAGE) was employed to display the de- letion mutations, and clones with differential length were selected to be sequenced. Sequence comparison was made to find the difference. Results: Two or three bands were displayed by PAGE in 60% patients. The results of sequence anal- ysis showed that there are some kinds of mutations in the BCP region. The substitution always occurs in TATA-like boxes, especially from T to C on 140 site. The deletion mutations were detected in TA1, TA2 and TA3. The 8bp, 20bp deletion mutations fre- quently happened. Conclusions: There is a hot deletion region in the BCP. The deletion and the substitution in the TATA- like box may influence the expression of preC/C pro- tein. The sequencing results indicate that there are HBV quasispecies groups in patients with chronic HBV infection.

Differential Proteomic Analysis of Carbon Ion Radiation in Sheep Sperm

This study is first to investigate proteomic changes in sheep sperm induced by carbon ion radiation using two-dimensional electrophoresis （2-DE） analysis in the project of breeding a new variety of sheep. Differential expression proteins were detected using the PDQuest 8.0 software after staining with Coomassie blue. Valid spots were then analyzed through liquid chromatography tandem mass spectrometry （LC-MS/MS）. Among the 480 total protein spots displayed in 2-D gels, 6 specific protein spots were observed in sperm gels. A search against protein sequences in the National Center for Biotechnology Information databases （NCBI） indicated that differentially expressed proteins correspond to two proteins, identified to be enolase and transcription factor AP-2-alpha （TFAP-2c0. The two proteins were up-regulated in the irradiated sperm. To the best of our knowledge, this study is the first to identify proteomic changes induced by carbon ion radiation in sheep sperm. The analysis of differential expression protein may be useful in identifying new breeding markers in sheep reproduction and in clarifying the mechanisms involved in irradiation or space breeding.

Molecular characterization of yolk proteins in the female crab Neptunus pelagicus(A.Milne-Edwards,1861) from the Mediterranean Sea of Alexandria,Egypt

This study aimed to characterize the morphological changes in the ovary of the female crab Neptunus pelagicus and to identify specific fractions of vitelloginin and vitelline molecules during primary and secondary vitellogenesis.Samples of the blue crab were collected from the Mediterranean Sea of Alexandria monthly during 2017.Ovaries and oocytes in primary and secondary vitellogenesis were detached and treated for histological test.Native polyacrylamide gel electrophoresis(PAGE)Bis-Tris Gels was applied to identify vitelloginin(VN)and vitelline(VL)molecules.Protein Analyses were done by PAGE-SDS.The initial degenerate primers were built regarding the conserved amino acid domains of the yolk proteins.Primary and secondary vitellogeneses consisted of 8 phases.Lipoprotein fraction with molecular weight 550 kDa was identified in the hemolymph in secondary vitellogenesis.Two protein fractions(VLI&VLII)were identified in secondary vitellogenic oocytes.The electrophoresis performed with extract of stage I oocyte showed two protein fractions with molecular weights 550 kDa and 460 kDa.In stage II and III oocyte,4 subunits were presented of 180,195,140 and 120 kDa in VLI and 2 subunits with molecular weight of 110 kDa and 95 kDa in VLII.Another two fractions in stage V oocyte presented with molecular weights of 380 kDa and 360 kDa.Western blot analysis proved that both fractions were of four major polypeptide subunits with molecular weight of 180,125,90 and 85 kDa in each of the two VLs.The hybridization signal obtained by the Northern blot was detected in the hepatopancreas during ovarian cycle and in the ovary during secondary vitellogenesis.The result of the reverse transcription-polymerase chain reaction(RT-PCR)analysis showed that the mRNA that encodes the C-terminal region of the VN cDNA was found in the ovary in secondary vitellogenesis and in the hepatopancreas.

High-throughput Three-dimensional Gel Electrophoresis for Versatile Utilities: A Stacked Slice-gel System for Separation and Reactions (4SR)

A novel high-throughput system, called the stacked slice-gel system for separation and reactions （4SR）, was developed for the analysis of DNA/RNA and protein/peptide. The system provides a novel three-dimensional gel electrophoresis approach that exploits the property of stacked slice gels. It allows multiple samples simultaneously to react as well as to be separated, offering a two-dimensional （m×n） sample loading system. For this purpose, high-throughput multi-micro vessels （MMVs） containing variable numbers of wells （100 wells in this paper） have been used, which are made of 25 mm square-size polyacrylamide gels. Furthermore, after electrophoretic separation, a slice gel containing a desired sample can be easily removed and proceeded to the next step. Different biological reactions as well as successive separation of products were effectively carried out dealing with DNA/RNA and protein/peptide. It shows that this system has a diversity of potentials to be developed.

Construction and Preliminary Analysis of Ovine Oocytes Proteomic 2-DE Map

[Objective] To obtain ovine oocytes 2-dimensional gel electrophoresis （2-DE） maps. [Method] Ovine oocytes were solubilized in lysis buffer, and protein concentrations were measured using the method of Bradford and Ramagli. Then the samples were subjected to two-dimensional polyacrylamide gel electrophoresis. The 2-DE maps of ovine oocytes were analyzed through PDQuest 8.0. [Resait] The Ramagli method could re- flect concentration of oocyte protein more actually and could optimize the quantity of samples to get a 2-DE map with higher quality. The protein concentration measured by the Bradford method was higher than its actual value. [Coclusion] Each 2-DE map loading 700 oocytes is more reasonable.

Effect of high salinity on cell growth and protein production of Antarctic ice microalgae Chlamydomonas sp. ICE-L

Antarctic ice microalgae Chlamydomonas sp.ICE-L can survive and thrive in Antarctic sea ice.In this study,Chlamydomonas sp.ICE-L could survive at the salinity of 132‰ NaCl.SDS-PAGE showed that the density of 2 bands（26 and 36 kD） decreased obviously at the salinity of 99‰ NaCl compared to at the salinity of 33‰ NaCl.The soluble proteins in Chlamydomonas sp.ICE-L grown under salinity of 33‰ and 99% NaCl were compared by 2-D gel electrophoresis.After shocking with high salinity,8 protein spots were found to disappear,and the density of 28 protein spots decreased.In addition,19 protein spots were enhanced or induced,including one new peptide（51 kD）.The changes of proteins might be correlated with the resistance for Chlamydomonas sp.ICE-L to high salinity.

Application of Two-Dimensional Electrophoresis in the Research of Retinal Proteins of Diabetic Rat

Diabetes mellitus （DM） is a chronic disease which is associated with numerous serious health complications such as diabetic retinopathy, and is the leading cause of new cases of blindness in adults at the age of 20-74 years old. The aim of the study was to establish and optimize a two-dimensional polyacrylamide gel electrophoresis （2-DE） technique for retina proteomics to improve the resolution and reproducibility, and to observe the proteomic changes of retinal tissues in diabetic and normal rats. Proteins were extracted from retinal tissues of normal and 8 weeks diabetic SD rats and used in two-dimensional electrophoresis. Various conditions of retina proteomic 2-DE were adjusted, optimized and protein spots of differential expression were obtained through analysis of 2-DE images with PDQuest software. By choosing appropriate sample amount, using pre-cast IPG dry strips （pH 5-8） and casting 12% equal gel, satisfactory 2-DE images of retina were obtained and a steady 2-DE technique was established. In this way, we found 36 spots in 2-DE gel of diabetic retinas that exhibited statistically significant variations, including up-regulation of 5 proteins in diabetic rat retinas, down-regulation of 23, and disappearance of 8, in comparison with normal tissues. The differences of protein expression were observed in retinas between diabetic and normal rats. Our established 2-DE technique of retina proteins could be effectively applied in proteomics of retina diseases. Cellular ＆ Molecular Immunology. 2007;4（1）：65-70.

Proteomic Alterations of Antarctic Ice Microalga Chlamydomonas sp.Under Low-Temperature Stress

Antarctic ice microalga can survive and thrive in cold channels or pores in the Antarctic ice layer. In order to understand the adaptive mechanisms to low temperature, in the present study we compared two-dimensional polyacrylamide gel electrophoresis （2-DE） profiles of normal and low temperature-stressed Antarctic ice microalga Chlamydomonas sp. cells. In addition, new protein spots induced by low temperature were identified with peptide mass fingerprinting based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-TOF-MS） and database searching. Well-resolved and reproducible 2-DE patterns of both normal and low temperature-stressed cells were acquired. A total of 626 spots was detected in control cells and 652 spots were detected in the corresponding low temperature-stressed cells. A total of 598 spots was matched between normal and stressed cells. Two newly synthesized proteins （a and b） in low temperature-stressed cells were characterized. Protein spot A （53 kDa, pl 6.0） was similar to isopropylmalate/homocitrate/citramalate synthases, which act in the transport and metabolism of amino acids. Protein spot b （25 kDa, pl 8.0） was related to glutathione S-transferase, which functions as a scavenger of active oxygen, free radicals, and noxious metabolites. The present study is valuable for the application of ice microalgae, establishing an ice microalga Chlamydomonas sp. proteome database, and screening molecular biomarkers for further studies.

Genetics analysis of haptoglobin gene in Fujian Han nationality

To study the genetic features(characteristics)of haptoglobin gene,four different age groups of Fujian Han people were investigated.The phenotypes of the hap-toglobin of four different groups were analyzed by using polyacrylamide gel electrophoresis.The frequency of Hp^(1) in the population of Fujian Han nationality accounted for 0.340,among which children,youths,middle aged and elder groups were 0.307,0.338,0.363 and 0.383,respect-ively.The Hp^(0-0)phenotype frequency was 0.026 in which the four age groups accounted for 0.032,0.046,0.014 and 0.014,respectively.The frequency of Hp^(1)gene is rising with increasing age.The frequency of Hp^(0-0)phenotype is highest in the middle aged group and then tends to drop with increasing age.

Evaluation,partial characterization and purification of acetylcholine esterase enzyme and antiangiogenic activity from marine sponges

Objective:To test three marine sponges Halichondria glabrata Keller,1891;Spirastrellapachyspira(S.pachyspira)Levi,1958 and Cliona lobata Hancock,1849 for the presence of the acetylcholinesterase(AChE)in both young and developed samples from western coastal area of India.S.pachyspira methanolic extract was selected for anti/pro angiogenic activity.Methods:They were evaluated for AChE activity using Ellman’s assay based on production of yellow colored 5-thio-2-nitrobenzoate.Purification of the enzyme was planned using ammonium sulphate precipitation and characterization by sodium dodecyl sulfate polyacrylamide gel electrophoresis.Chorioallantoic membrane(ChAM)assay model was used for angiogenic/antiangiogenic testing.Results:All the three sponges showed good specific enzyme activity and S.pachyspira contained maximum specific enzyme activity.Sixty percent of ammonium sulphate precipitation of crude protein sample gave single band at 66 kDa corresponding to the true AChE.ChAM assay was performed at 62.5,125.0 and 250.0μg/mL.Dosage beyond 250μg/mL extract showed toxic response with anti angiogenic activity at all the concentrations.Conclusions:AChE activity was detected in all samples.Extract showed good anti-angiogenic response at 62.5μg/mL.Extract was highly toxic affecting microvasculature of ChAM as well as normal growth and development of the embryo at 500μg/mL.With further characterization of bioactive compounds from the extract of S.pachyspira,the compounds can be developed for anti tumor activity.