Brachial artery aneurysm rupture in a patient with neurofibromatosis: a case report

Peripheral vascular manifestations of neurofibromatosis are rare but may result in fatal haemorrhaging when they rupture. Surgeons should be aware of this life-threatening condition. We report a case of 35-year-old woman with neurofibromatosis who presented with a swollen and tender mass around her right arm. Angiography revealed 2 aneurysms in the brachial artery. Surgical occlusion revealed a large amount of clotted blood within the subfascial space, and the bleeding point was identified as a pinpoint opening in the aneurysm. The brachial artery abutting the aneurysm and the surrounding soft tissues was extremely brittle and fragile, with massive oozing during dissection. The brachial artery was irreparable and was resected after ligation of the artery and surrounding soft tissues and the aneurysm. Despite an uneventful recovery, the patient died on day 4.

Dexamethasone coordinately regulates angiopoietin-1 and VEGF: a mechanism of glucocorticoid-induced stabilization of blood-brain barrier

Glucocorticoids stabilize the blood-brain barrier (BBB), leading to attenuation of vasogenic brain edema. However, the action mechanism of glucocorticoids has been poorly elucidated. To elucidate the mechanism, we investigated whether dexamethasone (Dex), a synthetic glucocorticoid hormone, regulates the levels of key permeability regulating factors such as angiopoietin-1, angiopoietin-2, and vascular endothelial growth factor (VEGF) in the three types of cells comprising BBB. Dex increased the level of angiopoietin-1 mRNA and protein and decreased VEGF mRNA and protein in brain astrocytes and pericytes, but not in endothelial cells. The mRNA and protein of angiopoietin-2 were detected only in endothelial cells and not regulated by Dex. The Dex-induced regulation of angiopoietin-1 and VEGF was inhibited by RU486, suggestive of glucocorticoid receptor mediation. The mRNA stability of angiopoietin-1 and VEGF was not changed by Dex treatment, implying that Dex increases angiopoietin-1 and decreases VEGF through transcriptional regulation. This is the first study showing the coordinate regulation of angiopoietin-1 and VEGF by glucocorticoids, suggesting a novel mechanism underlying glucocorticoids-induced stabilization of BBB.

Differential analysis of Bacillus anthracis after pX01 plasmid curing and comprehensive data on Bacillus anthracis infection in macrophages and glial cells

Bacillus anthracis is a gram-positive bacterial organism responsible for anthrax. This organism has two pathogenic plasmids: pX01 and pX02. The genetic function of pX01, which comprises about 198 kb, is not known, except for a region called the pathogenic island, which contains three genes-pag, lef, and cya-that code for three toxic proteins. A 2-D difference gel electrophoresis (2-D DIGE) system was used to verify the existence of proteins controlled by the pX01 plasmid, and protein regulation data were obtained using DeCyder software. A total of 1728 proteins were identified in the wild-type strain of this organism and 1684 in the pX01 plasmid. Twenty-seven of these proteins disappeared and eight appeared when the pX01 plasmid was removed. An additional 52 proteins were downregulated and 15 were upregulated when this plasmid was removed. A total of 102 proteins have been identified using the MALDI-TOF method of analysis, including 49 whose functions are unknown. Among these, 31 participate in metabolic processes, two in cellular processes, 15 in the processing of genetic information, and five in the processing of extracellular information. Another seven proteins participate in bacterial virulence and pathogenesis. We investigated the functions of these proteins in other bacteria, particularly the B. anthracis derivative H9041. Bacterial growth differed between pX01+/pX02+ B. anthracis and its pX01-/pX02+ derivative as did the cytotoxicity of macrophages infected by pX01+/pX02+ B. anthracis and the pX01-pX02+ derivative. We also found that S100B protein levels increased in the host infected with pX01+/pX02+ B. anthracis or its pX01-/pX02+ derivative. These data suggest that the pX01 plasmid plays a key role in the regulation of protein functions in B. anthracis.

Proteome of mesenchymal stem cells

Proteomics has evolved, in recent years, into effective tools for basic and applied stem cell research, and has been extensively used to facilitate the identification of changes in signal transduction components, especially with regard to plasticity, proliferation, and differentiation. Several recent reports have also employed proteomic strategies to characterize human mesenchymal stem cells (hMSC) and their differentiated derivatives. Although these approaches have yielded valuable data, the results highlight the fact that only the limited numbers of proteins are characterized at the protein level in these cells, thus necessitating expandable MSC proteome dataset. This review presents, for the first time, an expandable list of MSC proteins, which will function as a starting point for the generation of a comprehensive reference map of their proteome. Also, the better way to bridge current gap between genomics and proteomics study such as integrated proteomic and transcriptomic analyses is discussed.

Proteome analysis of the rat hepatic stellate cells under high concentrations of glucose

To study the change in hepatic stellate cell (HSC) function under diabetic conditions, we cultured rat HSC in the presence of 5 and 30 mM glucose, which correspond to blood glucose concentrations during the early and late stages of diabetes, respectively. The differentially expressed HSC proteins were analyzed using 2-DE and ESI-Q-TOF MS/MS and confirmed with Western blotting. The changed protein expression will provide greater understanding of glycolysis in HSC at the high concentration of glucose.

Evaluation of the biliary tract: The value of performing magnetic resonance cholangiopancreatography in conjunction with a 3-D spoiled gradient-echo gadolinium enhanced dynamic sequence

The 3-D gradient-echo (GRE) sequence allows thinner sections and better resolution of biliary obstruction. When the presence of biliary obstruction is identified using magnetic resonance cholangiopancreatography, the addition of the 3-D GRE sequence may be helpful for diagnosing biliary obstruction. By showing the changes in the bile duct wall, within the duct lumen and around the bile duct, this technique can be helpful for distinguishing benign from malignant stricture as well as a stone from an enhancing intraluminal mass.

The best candidates for transarterial chemotherapy in patients with hepatocellular carcinoma awaiting liver transplantation: a cohort-based characterization of dropout times

BACKGROUND

Although transarterial chemotherapy is used to retard tumour progression for hepatocellular carcinoma (HCC) patients awaiting orthotopic liver transplantation (OLT), information regarding the acceptable waiting time and appropriate patient selection for the therapy is lacking.

AIM

To examine dropout times and determine the best candidates for pre-transplant transarterial therapy in a cohort study.

METHODS

In total, 180 consecutive HCC candidates receiving pre-transplant chemo-lipiodolization were included in the study.

RESULTS

Overall, 70 (38.9%) patients dropped off the waiting list during the median follow-up of 19 months. According to the Child-Pugh (C-P) classification, the estimated dropout rates at 1 and 2 years were 17.2% and 44.8% for the C-P A group and 33.4% and 81.3% for the C-P B/C group, respectively. C-P B/C patients experienced more frequent dropouts than C-P A patients (P < 0.001). Risk factor analysis identified C-P classification to be the strongest predictor of dropout (P < 0.001). On multivariate analysis, alpha-fetoprotein (AFP) >100 ng/mL, tumour size >3 cm and multiple nodules remained independently predictive of dropout for C-P A group (all P < 0.05). Candidates with none of these factors were found to be at the lowest risk of dropout, with only a 22.5% dropout rate up to 41 months.

CONCLUSIONS

This study suggests that Child-Pugh A patients with one nodule <3 cm and AFP < 100 ng/mL may be the best candidates for pre-transplant chemo-lipiodolization, with the lowest dropout rate. However, comparative studies with other therapeutic options are needed to assess the definitive role of transarterial therapy in this setting.

Streptozotocin-induced diabetes can be reversed by hepatic oval cell activation through hepatic transdifferentiation and pancreatic islet regeneration

Hepatic oval cells have shown the potential to transdifferentiate into insulin-producing cells when cultured with high glucose concentrations. However, it remains unknown whether the oval cells can contribute to insulin production in diabetic mice. In this study, our aim was to investigate the response of activated hepatic oval cells to hyperglycemic conditions. C57BL/6 mice were fed a diet containing 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) for 4 weeks to activate the hepatic oval cell population before inducing hyperglycemia with streptozotocin (STZ). Despite the initial hyperglycemia (341+/-15 mg/dl), the blood glucose levels of DDC-STZ-treated mice were significantly improved within 6 weeks (185+/-12 mg/dl). During the initial hyperglycemic stage, DDC-STZ-treated livers expressed pancreatic developmental, endocrine and exocrine genes. Hepatic insulin production was confirmed by immunohistochemistry and ELISA. These results suggested that transdifferentiated hepatic oval cell population contributed to the amelioration of hyperglycemia. We additionally determined that DDC-STZ-treated pancreata played a critical role in complete reversal of hyperglycemia as evidenced by extensive beta-cell regeneration and increase of pancreatic insulin content after STZ treatment, which is rarely observed in other adult STZ models. Reversal of hyperglycemia in this model seems to be accomplished by biphasic insulin augmentation, first by hepatic transdifferentiation, and followed by endogenous beta-cell regeneration in the pancreas. The DDC-STZ treatment provides a novel injury model for better understanding of the functional behavior of hepatic and pancreatic stem/progenitor cell population under hyperglycemic condition, which may yield critical information for developing beta-cell-based therapies to treat diabetes.

Characterization of human insulin microcrystals and their absorption enhancement by protease inhibitors in rat lungs

Pulmonary route appears to be an attractive alternative as a non-invasive systemic delivery for peptide and protein drugs. An appropriate formulation, however, is important for increasing their bioavailability in lung. In this study, the human insulin microcrystals were produced. The particle size analysis and scanning electron microscopy (SEM) showed that the microcrystals were uniform and had a monodispersed size distribution (mean diameter = 0.95 microm) for pulmonary delivery. The physicochemical properties of the microcrystals developed were similar to those of the commercial crystalline powder in powder X-ray diffraction (XRD) and differential scanning calorimetry (DSC) analyses. The percentage of high molecular weight proteins (%HMWP), the percentage of other insulin related compounds (%OIRC) and the percentage of A-21 desamido insulin (%D) of the microcrystals were very low. In addition, the cytotoxicity of microcrystals developed and protease inhibitors (aprotinin, bacitracin and soybean-trypsin inhibitor) was investigated, and the enhancement of insulin absorption in the presence of these protease inhibitors at various concentrations was studied. The cell viability of A549 was over 80% at various concentrations of aprotinin and soybean-trypsin inhibitor, except for bacitracin (below 60%). The percent of decrease in blood glucose (D%) was 42.68+/-1.62% after intratracheal instillation of insulin microcrystals (5 U/kg). An enhancement of hypoglycemic effect with protease inhibitors was also found. Soybean-trypsin inhibitor (48.86+/-3.24% at 10 mg/ml; 55.78+/-0.71% at 5 mg/ml; 51.49+/-5.27% at 1 mg/ml) and aprotinin (52.57+/-8.78% at 10 mg/ml; 51.97+/-1.98% at 5 mg/ml; 56.90+/-3.42% at 1 mg/ml) were effective for absorption enhancement. These findings suggest that the use of insulin microcrystals and protease inhibitors would be useful to improve the hypoglycemic effect in pulmonary route.

Comparison of proteomes in various human plasma preparations by two-dimensional gel electrophoresis

Serum or plasma can be utilized in a variety of studies targeted toward the discovery of disease biomarkers. In this study, the proteome profiles of plasma samples prepared using various anticoagulants (EDTA, heparin or citrate), were compared with those of serum using two-dimensional electrophoresis (2-DE). Proteins which evidenced different levels in the plasma and serum were screened and identified using ESI-Q-TOF MS/MS. The proteins which became detectable after the removal of fibrinogen from serum were identified as pigment epithelial differentiating factor (four spots), fetuin-like protein, and the hemopexin precursor. In particular, three proteins, pre-serum amyloid P component, plasma glutathione peroxidase precursor, and tetranectin, evidenced increased volume intensity only in the plasma samples prepared with EDTA.

Functional characterization of Hsp33 protein from Bacillus psychrosaccharolyticus; additional function of HSP33 on resistance to solvent stress

Psychrophiles have been known as efficient organism to degrade organic solvent. To investigate the mechanism of solvent stress and identify the factors that affect the solvent stress in psychrophiles, we selected Bacillus psychrosaccharolyticus one of the psychrophiles and two-dimensional gel electrophoresis was performed. Among the protein spots analyzed by 2-DE, five spots induced in 3% IPA stress conditions were identified by MS/MS, and one of these spots was identified as a Hsp33 family. The Hsp33 protein sequence of B. psychrosaccharolyticus exhibited a high similarity with the corresponding proteins of other bacteria. The Hsp33 protein of B. psychrosaccharolyticus has a highly conserved zinc-binding domain (CXCX, CXXC) that includes four cysteine residues in the C-terminus. In addition, the transcriptional induction of the HSP33 of B. psychrosaccharolyticus was confirmed by Northern blot analysis, and formation of free thiol linkage was induced under stress conditions such as exposure to solvents, heat-shock, and oxidative stress. Furthermore, over-expressed strains of HSP33 of B. psychrosaccharolyticus in Escherichia coli improved stress tolerance to the organic solvent when compared with the wild-type. These data suggest that the solvent stress condition was similar to heat-shock or oxidative stress, especially through the triggering of induction and activation of a redox-regulatory chaperone, Hsp33, and Hsp33 plays a critical role in the tolerance to stress.

Human blood plasma preparation for two-dimensional gel electrophoresis

Human plasma consists of mainly large proteins, which vary in terms of both composition and concentration with the physiological state of the individual. Alterations in protein concentrations reflect the current state of the individual's health and thus may be utilized as valuable biomarkers for a specific biological process or disease. Two-dimensional gel electrophoresis (2-DE) has proven to be a valuable method for the separation and comparison of complex protein mixtures, for example, from disease and healthy states, as this method provides information regarding the variation, relative quantities, and structures of the intact proteins. The procedures utilized for the preparation of samples for 2-DE are critical to the acquisition of high-quality results for the discovery of biomarkers. The objective of this study was to review the preparation methods of plasma for 2-DE, particularly those designed to improve the detection of proteins in low abundance in plasma on 2-DE. The use of anticoagulants and protease inhibitors during the collection of blood, the removal of abundant proteins using multicomponent immunodepletion system, and desalting procedure allow us to compile profiles of proteins occurring in low concentrations in the plasma and to improve the pattern generated during 2-DE.

Helicobacter pylori eradication for low-grade gastric mucosa-associated lymphoid tissue lymphoma is more successful in inducing remission in distal compared to proximal disease

A series of studies has shown that Helicobacter pylori eradication induces remission in most patients with low-grade gastric mucosa-associated lymphoid tissue (MALT) lymphoma. However, there have been few reports about the effect of bacterial treatment on the gastric MALT lymphoma in Korea, a well-known H. pylori endemic area. A total of 111 H. pylori-infected patients were prospectively enrolled in Seoul National University Hospital and 99 among them were completely followed up according to our protocol. After H. pylori eradication, tumoural response was evaluated by endoscopy and histopathology every 2–3 months till complete remission (CR) and every 6 months after achieving CR. Median follow-up period was 41 months (range, 11–125 months). Helicobacter pylori was successfully eradicated in all 99 patients and CR was obtained in 84 (84.8%) of 99 patients. The median time to reach CR was 3 months and 94% of CR is in continuous complete remission. Five patients with CR relapsed after 10–22 months without the evidence of H. pylori reinfection. Cumulative recurrence rate was 2.3, 7.7 and 9.3% at 1, 2 and 3 years, respectively. Tumours were mainly located in distal stomach (67.7%) and tumours in distal stomach were associated with more favourable response than those in proximal stomach (P=0.001). Majority of patients with low-grade gastric MALT lymphoma treated by exclusive H. pylori eradication have a favourable long-term outcome, offering a real chance of cure. Tumour location could be a predictive factor for remission following H. pylori eradication.

Proteome analysis of serum from type 2 diabetics with nephropathy

Diabetic nephropathy (DN) is a renal disease which develops as a consequence of diabetes mellitus. Microalbuminuria is the earliest clinical sign of DN. There are no specific diagnostic biomarkers for type 2 diabetics with nephropathy other than microalbuminuria and macroalbuminuria. However, microalbuminuria does not constitute a sole independent indicator for type 2 diabetics with nephropathy, and thus, another screening method, such as a biomarker assay, is required in order to diagnose it more correctly. Therefore, we have utilized two-dimensional electrophoresis (2-DE) to identify human serum protein markers for the more specific and accurate prediction of progressive nephropathy in type 2 diabetes patients, via comparisons of the serum proteome in three experimental groups: type 2 diabetes patients without microalbuminuria (DM, n = 30), with microalbuminuria (MA, n = 29), and with chronic renal failure (CRF, n = 31). As a result, proteins which were differentially expressed with statistical significance (p < 0.05) in MA and CRF groups as compared to those in DM group were selected and identified by ESI-Q-TOF MS/MS. Among these identified proteins, two proteins which might be useful as diagnostic biomarkers of type 2 diabetics with nephropathy were verified by Western blotting: extracellular glutathione peroxidase (eGPx) and apolipoprotein (ApoE) were found to exhibit a progressive reduction in MA and CRF groups. Notably, eGPx was further verified by ELISA using DM (n = 100) and MA (n = 96) patient samples. Collectively, our results show that the two proteins identified in this study may constitute potential biomarkers for the diagnosis of type 2 diabetics with nephropathy.

The discovery of biomarkers for type 2 diabetic nephropathy by serum proteome analysis

Diabetic nephropathy (DN) is a serious kidney complication of diabetes, and constitutes the leading cause of end-stage renal disease. The earliest clinical evidence of DN is microalbuminuria, a term which refers to the appearance of small but abnormal amounts of albumin in the urine. However, screening methods for DN, such as biomarker assays, are yet to be developed for type 2 DN. In the present study, in an attempt to identify the biomarkers for initial diagnoses of type 2 DN, the protein profiles of human sera collected from 30 microalbuminuric type 2 diabetic patients were compared with those collected from 30 normoalbuminuric type 2 diabetic patients, via 2-DE. As a result, a total of 18 spots were determined to have different protein levels in the microalbuminuric patients. Twelve spots had lower protein levels of approximately 50%, and the other six had higher levels of approximately 100-300% as compared to the spots of normoalbuminuric patients. These spots were identified with ESI-Q-TOF (ESI-quadrupole-TOF) MS. Among the identified proteins, vitamin D-binding protein (DBP) and pigment epithelium-derived factor (PEDF) were verified by Western blotting. The results of this study indicate that the DBP may be employed as diagnostic and monitoring biomarkers of type 2 DN, contingent on further study into the matter.

Proteome analysis of Halobacterium salinarum and characterization of proteins related to the degradation of isopropyl alcohol

We reported in a previous study that proteomic approach, coupled with genomic techniques, could be used to screen and develop multiple candidates for halophilic enzymes from Halobacterium salinarum. In order to evaluate the biodegradation of isopropyl alcohol (IPA) by H. salinarum, the amounts of residual IPA and acetone generated in the growth media were determined using a gas chromatography-flame ionization detector (GC-FID). The protein expression profiles of cells which had been cultured with IPA were obtained with the two-dimensional gel electrophoresis. Proteins evidencing different expression levels in the presence of 0.5% IPA were identified by electrospray ionization-quadruple-time of flight (ESI-Q-TOF) mass spectrometry. We found 12 proteins which were down-regulated, and another 12 proteins which were up-regulated, in the presence of 0.5% IPA and we further identified 17 proteins among them using ESI-TOF MS/MS. Among these identified proteins, we selected glyceraldehyde 3-phosphate dehydrogenase (GAPDH) for further characterization as a halophilic enzyme. We have demonstrated for the first time that H. salinarum possesses the ability to degrade IPA and GAPDH was both stable and active at high salt concentrations, with maximum activity occurring at 1 M NaCl, although the optimal salt concentration with regard to the growth of H. salinarum is 4.3 M.

Better understanding of the filtration characteristics in the flexible fibre filter module (3FM)

This study is about the particle retention and filtration characteristics of fibre filter. Four laboratory scale fibre filters with different heights were used in parallel at various packing densities and filtration velocities. Of all of the operating parameters studied, filtration velocity had the most influence. Contrary to general theories, pressure drop increases slightly during the filtration in spite of the continuous retention of particles. This may have occurred because of large porosity of the packing (about 93%). This might be considered an advantage of the filter and something that makes it economic. The higher the filtration velocity, the larger the mass of particles retained in the filter. For filtration velocities of 20 and 40 m/h, particles smaller than 5 microm are retained as proven by the particle size distribution at the inlet and outlet.

Glioblastoma cell death induced by asiatic acid

Asiatic acid (AA), a triterpene, is known to be cytotoxic to several tumor cell lines. AA induces dose- and time-dependent cell death in U-87 MG human glioblastoma. This cell death occurs via both apoptosis and necrosis. The effect of AA may be cell type-specific as AA-induced cell death was mainly apoptotic in colon cancer RKO cells. AA-induced glioblastoma cell death is associated with decreased mitochondrial membrane potential, activation of caspase-9 and -3, and increased intracellular free Ca2+. Although treatment of glioblastoma cells with the caspase inhibitor zVAD-fmk completely abolished AA-induced caspase activation, it did not significantly block AA-induced cell death. AA-induced cell death was significantly prevented by an intracellular Ca2+ inhibitor, BAPTA/AM. Taken together, these results indicate that AA induces cell death by both apoptosis and necrosis, with Ca2+-mediated necrotic cell death predominating.

Crystallization of antiangiogenic Kringle V derived from human apolipoprotein A: crystallization applied to purification and formulation

In this study, the Kringle V domain (Glu4225-Ser4310) of human apolipoprotein A, an antiangiogenic polypeptide, was expressed as a secreted form in Pichia pastoris, and was purified via a process consisting of three chromatographic steps. The chromatographically purified kringle V domain contained a C-terminal serine-deleted form and several high-molecular-weight forms, which were suspected to represent glycosylated derivatives. In order to remove these derivatives, we employed a crystallization process. The crystallization of kringle V resulted in an 85% recovery yield, and also resulted in the complete removal of the aforementioned high-molecular-weight forms. However, we were still able to detect a trace of the C-terminal serine-deleted form. The prepared Kringle V crystals were stable within a pH range of 7.0 to 8.0, and were completely dissolved by dilution, which is a crucial factor in the preparation of a highly concentrated formulation. The chromatogram of the crystallized kringle V on reversed-phase HPLC analysis was identical to that observed without crystallization. Also, we noted that the original anti-wound migration activities of the molecule toward human umbilical vein endothelial cells were completely retained.

Overexpression of alpha1-protease inhibitor and galectin-1 in radiation-induced early phase of pulmonary fibrosis

PURPOSE

Radiation-induced pulmonary fibrosis (RIF) is a significant complication of radiotherapy for lung cancer. Despite the large number of studies, the molecular mechanisms of RIF are poorly understood. Therefore, the complex protein expression pattern in RIF was characterized by identifying the proteins with an altered expression level after thorax irradiation using two-dimensional electrophoresis (2-DE) and mass spectrometry.

MATERIALS AND METHODS

A mouse model of RIF was used to examine the alteration of the lung proteome because of availability of murine data related to human cases and the abundance of murine fibrotic lung samples. A mouse model of RIF was induced in radiosensitive C57BL/6 mice. Twenty-one weeks after 25 Gy irradiation, hematoxylin-eosin staining and hydroxyproline assay confirmed the early-phase pulmonary fibrosis.

RESULTS

Lung samples from the irradiated and age-matched control mice were used to generate 16 high quality 2-DE gels containing approximately 1,000 spots. Of the 31 significantly up- or down-regulated protein spots, 17 were identified by MALDI-TOF/MS.

CONCLUSIONS

Two important upregulated proteins were found, the alpha1-protease inhibitor and galectin-1, which might be used as potential markers for the early phase of RIF.

Halophile aldehyde dehydrogenase from Halobacterium salinarum

Halobacterium salinarum is a member of the halophilic archaea. In the present study, H. salinarum was cultured at various NaCl concentrations (3.5, 4.3, and 6.0 M NaCl), and its proteome was determined and identificated via proteomics technique. We detected 14 proteins which were significantly down-regulated in 3.5 M and/or 6 M NaCl. Among the identified protein spots, aldehyde dehydrogenase (ALDH) was selected for evaluation with regard to its potential applications in industry. The most effective metabolism function exhibited by ALDH is the oxidation of aldehydes to carboxylic acids. The ALDH gene from H. salinarum (1.5 kb fragment) was amplified by PCR and cloned into the E. coli strain, BL21 (DE3), with the pGEX-KG vector. We subsequently analyzed the enzyme activity of the recombinant ALDH (54 kDa) at a variety of salt concentrations. The purified recombinant ALDH from H. salinarum exhibited the most pronounced activity at 1 M NaCl. Therefore, the ALDH from H.salinarum is a halophilic enzyme, and may prove useful for applications in hypersaline environments.

The proteomic analysis of an adipocyte differentiated from human mesenchymal stem cells using two-dimensional gel electrophoresis

Adipose tissues play a crucial endocrine role in the control of whole body glucose homeostasis and insulin sensitivity. Considering the current substantial rise in obesity and obesity-related diseases, including diabetes, it is important to understand the molecular basis of adipocyte differentiation and its control. In this study, we have analyzed the protein expression inherent to adipogenic differentiation, by 2-DE, MALDI-TOF, and RT-PCR. This study focused on proteins that were differentially expressed by the differentiation of human mesenchymal stem cells (hMSCs) to adipocytes. We conducted 2-DE for each set of proteins in the cytosol of adipocytes that had differentiated from hMSC, in a pH range from 3-10. Thirty-two protein spots were shown to have different expression levels. Among these, eight up-regulated proteins were identified by MALDI-TOF/MS, as the following: syntaxin binding protein 3, OSBP-related protein 3, phosphodiesterase, glycophorin, immunoglobulin kappa chain variable region, peroxisome proliferative activated receptor gamma (PPAR-gamma), bA528A10.3.1 (novel protein similar to KIAA01616, isoform 1), and T cell receptor V-beta 4. Four proteins: syntaxin-3, OSBP-related protein 3, PPAR-gamma and glycophorin were associated with adipogenesis.

Monitoring of pH inhibition on microbial activity in a continuous flow reactor by pseudo toxic concentration (C(PT)) concept and time delay model

The pseudo toxic concentration (C(PT)) concept was introduced as a quantification method to describe pH as an inhibitor concentration. In this research, the applicability of the C(PT) concept model for the detection of pH inhibitions was expanded for a continuous flow activated sludge reactor. A pilot equipped with an inhibition detection system was installed. Inhibitory wastewater was injected for 1 h and the relative activity was calculated by the maximum respiration rate. At the same time, the coefficients for the C(PT) concept model were estimated. At the dynamic conditions, the estimated relative activity by the C(PT) concept model showed time lag compared to the measured one. However, the time lag problem was successfully resolved by introducing a transfer function into the C(PT) concept model. The C(PT) concept model combined with a transfer function (C(PT) + TF model) successfully tracked the variation of the relative activity under dynamic conditions. The C(PT) + TF model could detect 50% inhibition faster than the respirometry based method by approximately 10 min. Moreover, it had additional advantages such as being inexpensive, easy to install and simple to operate. In conclusion, the C(PT) + TF model was an effective and convenient detection method of pH inhibition.

Practical approach to parameter estimation for ASM3+ bio-P module applied to five-stage step-feed EBPR process

Various parameter optimization approaches to a five-stage step-feed EBPR process modeled using the ASM3+bio-P module were examined. Five stoichiometric (Y(STO,NO), Y(H,O2, Y(H,NO,) Y(PAO,O2), Y(PO4)) and seven kinetic parameters (k(STO), eta(NO), b(H), mu(max),PAO, q(PHA), q(PP), mu(max),A) were estimated. The optimization approaches could be classified based on the data sources (batch experiments or CSTR operation data) and the number of target variables used in calculating the objective function. Optimized parameter values obtained by each approach were validated with CSTR operation data that were not used for parameter optimization. The results showed that the parameter optimization only with batch experimental results could not be directly applied to CSTR operation data. ASM3 + bio-P module parameters could be finely optimized only with CSTR operation data when sufficient target variables for objective function calculation were applied. When the number of target variables was increased, prediction performance was significantly improved. Once optimized, the model was able to predict the characteristic features of the five-stage step-feed process; namely, a high PAO yield, fast PAO growth, fast X(pp) storage, slow X(STO) and X(PHA) storage.

Rule-based fuzzy inference system for estimating the influent COD/N ratio and ammonia load to a sequencing batch reactor

A fuzzy inference system using sensor measurements was developed to estimate the influent COD/N ratio and ammonia load. The sensors measured ORP, DO and pH. The sensor profiles had a close relationship with the influent COD/N ratio and ammonia load. To confirm this operational knowledge for constructing a rule set, a correlation analysis was conducted. The results showed that a rule generation method based only on operational knowledge did not generate a sufficiently accurate relationship between sensor measurements and target variables. To compensate for this defect, a decision tree algorithm was used as a standardized method for rule generation. Given a set of inputs, this algorithm was used to determine the output variables. However, the generated rules could not estimate the continuous influent COD/N ratio and ammonia load. Fuzzified rules and the fuzzy inference system were developed to overcome this problem. The fuzzy inference system estimated the influent COD/N ratio and ammonia load quite well. When these results were compared to the results from a predictive polynomial neural network model, the fuzzy inference system was more stable.

Identification of the adverse effect of nitrate on the phosphate release rate and improvement of EBPR process models

The adverse effect of nitrate on the phosphate release rate in the anaerobic phase was observed and was hardly explainable with conventional EBPR process models. Four possible mechanisms were proposed including substrate competition, reduced fermentation, parallel reaction and sequential reaction. Batch experiments were designed and conducted to identify the dominant mechanism. Results showed that the sequential reaction was the only possible mechanism where only denitrification occurred if any nitrate existed in the anaerobic phase. Then the phosphate release following after the nitrate was completely removed. Nitrate inhibition effect was added into the PHA storage rate to incorporate the sequential reaction in the conventional ASM3 plus EAWAG bio-P module (ASM3 + P). Nitrate inhibition coefficient, K(I,NO,PAO) was found to be as low as 0.05 mg/L. This correlated well with experimental observation where no also meant that the anaerobic compartment of a continuous flow reactor could be seriously affected by the residual nitrate contained in the sludge recycle flow. This phenomenon caused overestimation of the phosphate uptake rate and consequently underestimation of PO4(3-) -P concentration. This problem was resolved by incorporation of a nitrate inhibition term in the ASM3 + P for more accurate simulation of the EBPR process.

Enhancing flexible fiber filter (3FM) performance using in-line coagulation

A new packing for deep bed filtration using Flexible Fibers has been proposed and developed on a very large scale for tertiary treatment of wastewater. The purpose of this study is to check the possibility of using this technology for the production of drinking water from surface water. In this study, the feasibility of the fiber filter application on water treatment was examined and the removal efficiency of fiber filter was improved using an in-line coagulant injection method. The experiments were carried out at pilot scale. The filter was packed with bundles of polyamide fibers with a bed porosity of 93%. Nak-dong River was used as the filter influent water and alum, PSOM, and PAC were used as the coagulants. The coagulants were injected by the in-line injection method. Small dosages (1-5 mg/L) of the polymeric coagulants (PSOM and PAC) showed an increase of removal efficiency compared to the operation without coagulants. Specifically, 1 mg/L of PAC showed the longest filtration time. Considering filtration time, filtrate quality, and filtered volume, the filtration velocity of 120 m/hr was chosen as an optimum value. For long-term operations, the effluent quality was 0.4 NTU and the removal efficiency was stable for the given optimum conditions.

Equipment fault diagnosis system of sequencing batch reactors using rule-based fuzzy inference and on-line sensing data

The importance of a detection technique to prevent process deterioration is increasing. For the fast detection of this disturbance, a diagnostic algorithm was developed to determine types of equipment faults by using on-line ORP and DO profile in sequencing batch reactors (SBRs). To develop the rule base for fault diagnosis, the sensor profiles were obtained from a pilot-scale SBR when blower, influent pump and mixer were broken. The rules were generated based on the calculated error between an abnormal profile and a normal profile, e(ORP)(t) and e(DO)(t). To provide intermediate diagnostic results between "normal" and "fault", a fuzzy inference algorithm was incorporated to the rules. Fuzzified rules could present the diagnosis result "need to be checked". The diagnosis showed good performance in detecting and diagnosing various faults. The developed algorithm showed its applicability to detect faults and make possible fast action to correct them.

Parameter sensitivity analysis for activated sludge models No. 1 and 3 combined with one-dimensional settling model

The aim of this study was to suggest a sensitivity analysis technique that can reliably predict effluent quality and minimize calibration efforts without being seriously affected by influent composition and parameter uncertainty in the activated sludge models No. 1 (ASM1) and No. 3 (ASM3) with a settling model. The parameter sensitivities for ASM1 and ASM3 were analyzed by three techniques such as SVM-Slope, RVM-SlopeMA, and RVM-AreaCRF. The settling model parameters were also considered. The selected highly sensitive parameters were estimated with a genetic algorithm, and the simulation results were compared as deltaEQ. For ASM1, the SVM-Slope technique proved to be an acceptable approach because it identified consistent sensitive parameter sets and presented smaller deltaEQ under every tested condition. For ASM3, no technique identified consistently sensitive parameters under different conditions. This phenomenon was regarded as the reflection of the high sensitivity of the ASM3 parameters. But it should be noted that the SVM-Slope technique presented reliable deltaEQ under every influent condition. Moreover, it was the simplest and easiest methodology for coding and quantification among those tested. Therefore, it was concluded that the SVM-Slope technique could be a reasonable approach for both ASM1 and ASM3.

Forecasting influent flow rate and composition with occasional data for supervisory management system by time series model

The information on the incoming load to wastewater treatment plants is not often available to apply modelling for evaluating the effect of control actions on a full-scale plant. In this paper, a time series model was developed to forecast flow rate, COD, NH4(+)-N and PO4(3-)-P in influent by using 250 days data of field plant operation data. The data for 150 days and 100 days were used for model development and model validation, respectively. The missing data were interpolated by the spline method and the time series model. Three different methods were proposed for model development: one model and one-step to seven-step ahead forecasting (Method 1); seven models and one-step-ahead forecasting (Method 2); and one model and one-step-ahead forecasting (Method 3). Method 3 featured only one-step-ahead forecasting that could avoid the accumulated error and give simple estimation of coefficients. Therefore, Method 3 was the reliable approach to developing the time series model for the purpose of this research.

Purification and characterization of a recombinant anti-angiogenic kringle fragment expressed in Escherichia coli: Purification and characterization of a tri-kringle fragment from human apolipoprotein (a) (kringle IV (9)–kringle IV (10)–kringle V)

A kringle fragment (type IV (9)-IV (10)-V) from human apolipoprotein (a) (called LK68) was expressed in an inclusion body in Escherichia coli. The LK68 in this inclusion body was rendered soluble with urea, and efficiently refolded via oxidation in the presence of re-dox couple. The refolded LK68 was then purified via two steps of ion exchange chromatography, concentrated via preparative reversed-phase chromatography, and freeze-dried, at a final yield of approximately 30%. The purified LK68 exhibited profound affinity for lysine and fibrinogen, which suggests the proper folding of the kringle fragment, and also indicates that the native characteristics of apolipoprotein (a) were preserved. The purified LK68 was determined to be highly homogeneous upon reversed-phase HPLC analysis and size-exclusion HPLC analysis, in the presence of 20% (v/v) acetonitrile. However, on size-exclusion HPLC analysis without acetonitrile, it was determined to be somewhat heterogeneous, and this was corroborated by native analyses, including native PAGE and IEF.

Full-cyclic control strategy of SBR for nitrogen removal in strong wastewater using common sensors

A full-cyclic automatic control strategy for sequencing batch reactors (SBR) was proposed using only common sensors such as ORP, DO and pH. The main objective was to develop a generally applicable and robust control strategy. To accomplish this, various control schemes found in the literature or suggested by authors were examined at diverse ammonia loads and SCOD/NH4(+)-N ratios. Advantages and constraints of each scheme were discussed and compared. Ammonia load was estimated with DO lag time during the aerobic stage, and then the influent pump was manipulated to meet the desired load at the next anoxic stage. A partial denitrification scheme was chosen for the anoxic stage period control, to save anoxic time and external carbon. For external carbon dosage control, intermittent feeding at each anoxic stage was concluded to be a suitable scheme. The anoxic stage period could be successfully controlled by the combination of pH increase and DO increase. Every suggested control scheme was incorporated into a full-cyclic control strategy and tested at 0.02, 0.035, 0.08 kg NH4(+)-N/m3/sub-cycle. From the results, it is expected to perform unmanned automatic SBR operation with this strategy.

Expression and prognostic implications of cell cycle regulatory molecules, p16, p21, p27, p14 and p53 in germinal centre and non-germinal centre B-like diffuse large B-cell lymphomas

AIMS

To evaluate the different expression patterns and the prognostic significance of cell cycle regulatory molecules in diffuse large B-cell lymphomas (DLBCLs) of germinal centre (GC) and non-GC phenotypes.

METHODS AND RESULTS

Tissue microarray slides composed of 126 extranodal and 88 nodal DLBCLs were immunostained for p16, p21, p27, p14 and p53. DLBCLs were classified into GC and non-GC phenotype according to the immunohistochemical expression of bcl-6, CD10, and MUM1. Aberrant expression of p53 was more frequent in the GC phenotype in nodal cases (P = 0.038), and the loss of p16, p21 and p14 expression was significantly more common in the non-GC phenotype (P = 0.004, P = 0.001, P < 0.001). Concurrent disruptions of the p16-Rb and p14-p53 pathways as represented by the immunoprofile of p16/p14/p53 (-/-/+) were associated with a poor prognosis in the GC phenotype [mean survival 31 months in the p16/p14/p53 (-/-/+) group versus 62 months in the other groups, P =0.0485].

CONCLUSIONS

The expression and prognostic implications of cell cycle regulatory molecules differ between GC and non-GC phenotypes in DLBCLs. The immunoprofile of p16/p14/p53 (-/-/+) within the GC phenotype of DLBCLs can be defined as a poor prognostic subgroup.

Crystallization and preliminary X-ray crystallographic analysis of human RGS10 complexed with Galphai3

G-protein-coupled receptors, which are major targets for drug discovery, play a major role in diverse physiological processes by relating changes in the extracellular environment to intracellular functions via activation of heterotrimeric G-proteins. However, G-protein activity is also modulated by a family of proteins called regulators of G-protein signalling (RGS), which are classified into six subfamilies. RGS10 belongs to the subgroup D/R12 and is known to act specifically on activated forms of three Galpha proteins (Galphai3, Galphaz and Galphao but not Galphas). It is abundantly expressed in brain and immune tissues and has been implicated in the pathophysiology of schizophrenia. The RGS domain of RGS10 was cloned, purified, complexed with human Galphai3 and crystallized. The crystals containing both RGS and Galphai3 belong to space group P4(3)2(1)2 (or P4(1)2(1)2), with unit-cell parameters a = 99.88, b = 99.88, c = 144.59 A, alpha = beta = gamma = 90 degrees . A full set of diffraction data were collected to 2.5 A resolution at 100 K using synchrotron radiation at Pohang beamline 4A.

In vitro trans-differentiation of rat mesenchymal cells into insulin-producing cells by rat pancreatic extract

Recent reports have suggested that mesenchymal cells derived from bone marrow may differentiate into not only mesenchymal lineage cells but also other lineage cells. There is possibility for insulin-producing cells (IPCs) to be differentiated from mesenchymal cells. We used self-functional repair stimuli of stem cells by partial injury. Rat pancreatic extract (RPE) from the regenerating pancreas (2 days after 60% pancreatectomy) was treated to rat mesenchymal cells. After the treatment of RPE, they made clusters like islet of Langerhans within a week and expressed four pancreatic endocrine hormones; insulin, glucagon, pancreatic polypeptide, and somatostatin. Moreover, IPCs released insulin in response to normal glucose challenge. Here we demonstrate that the treatment of RPE can differentiate rat mesenchymal cells into IPCs which can be a potential source for the therapy of diabetes.

Plasma Protein Level Changes in Waste Incineration Workers Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin

TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) is a chemical compound which is known to induce severe reproductive and developmental problems, immune system damage, and interference with regulatory hormones. To characterize changes in the expression of plasma proteins caused by exposure to TCDD, we analyzed plasma samples from workers at municipal incinerators using two-dimensional gel electrophoresis (2-DE). Proteins exhibiting differences in expression were identified by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) and electrospray ionization quadrupole (ESI-Q) TOF mass spectrometry. One newly expressed protein was identified as the adrenomedulin binding protein (AMBP). Seven overexpressed proteins were identified in this study, and the most overexpressed protein was identified as alpha-fetoprotein (AFP). In addition, we cultured HepG2 cells in the presence of TCDD, to determine the effects of TCDD on the AFP and albumin expression in mRNA and protein levels, via RT-PCR and Western blotting, respectively. TCDD treatment resulted in an increase in the mRNA and protein expression levels of AFP, but reduced albumin expression. According to our results, exposure to TCDD may induce liver disease or cancer, and the proteins identified in this study could help reveal the mechanisms underlying TCDD toxicity.

Comparative Analysis of the Tear Protein Expression in Blepharitis Patients Using Two-Dimensional Electrophoresis

Change in the expression of body fluid proteins is caused by many diseases or environmental disturbances. The changes in tear proteins are also associated with various pathological eye conditions. Especially, chronic blepharitis is one of the most common conditions seen in the ophthalmologist's office. However, there are no specific clinical diagnostic tests for blepharitis, and it is difficult to treat effectively. Therefore, the aim of this study was to screen prognostic or diagnostic marker tear proteins for blepharitis and investigate pathogenesis of this disease using proteomics techniques. The tear proteins expressed in patients suffering from blepharitis (patient, n=19) and healthy volunteers (control, n=27) were analyzed using the two-dimensional electrophoresis (2-DE) technique. The differentially expressed proteins in patients were identified with ESI-Q-TOF (electrospray-quadrupole-time-of-flight) mass spectrometry and confirmed with western blotting. Nine proteins in patient were down regulated about 50% compared to those of the control: serum albumin precursor, alpha-1 antitrypsin, lacritin precursor, lysozyme, Ig-kappa chain VIII, prolactin inducible protein (PIP/GCDFP-15), cystatin-SA III, pyruvate kinase, and an unnamed protein. The use of the two-dimensional eletrophoretic technique could give more insight into the disease-related protein expression changes in tear fluids. Our findings reveal that the composition of tear proteins in blepharitis patients is different from that of healthy subjects and may provide further insights into the pathogenesis of blepharitis.

Proteomics of Halophilic archaea

Halophilic archaea is a member of the Halobacteriacea family, the only family in the Halobacteriales order. Most Halophilic archaea require 1.5M NaCl both to grow and retain the structural integrity of the cells. The proteins of these organisms have thus been adapted to be active and stable in the hypersaline condition. Consequently, the unique properties of these biocatalysts have resulted in several novel applications in industrial processes. Halophilic archaea are also to be useful for bioremediation of hypersaline environment. Proteome data have expended enormously with the significant advance recently achieved in two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). The whole genome sequencing of Halobacterium species NRC-1 was completed and this would also provide tremendous help to analyze the protein mass data from the similar strain Halobacterium salinarum. Proteomics coupled with genomic databases now has become a basic tool to understand or identify the function of genes and proteins. In addition, the bioinformatics approach will facilitate to predict the function of novel proteins of Halophilic archaea. This review will discuss current proteome study of Halophilic archaea and introduce the efficient procedures for screening, predicting, and confirming the function of novel halophilic enzymes.

Proteome analysis of rat pancreas induced by pancreatectomy

The previous study demonstrated that the streptozotocin (STZ)-induced diabetic mice can be cured by injecting the regenerating pancreatic extract (RPE) of the partially pancreatectomized Wistar-Kyoto rats. In this study, to characterize the complex pattern of protein expression in RPE, the proteins of altered expression level after the pancreatectomy were identified by 2-dimensional electrophoresis (2-DE) and mass spectrometry. Of 76 significantly up- or down-regulated protein spots, 61 were identified by MALDI-TOF/MS. Moreover, the whole RPE was fractionated into 4 groups using an anion-exchange chromatography and each fraction's cell proliferating activity was measured by MTT assay. Compared to the normal pancreatic extract, fraction 3 and 4 of RPE showed the maximal cell proliferating activity. On 2-DE of 3 and 4 fractions, a total of 10 spots, which are differentially expressed after the pancreatectomy, were identified by MS/MS. Of these identified proteins, Reg III which might be functionally associated with well known regenerating factor (Reg I) was found. Taken together, our results demonstrated that the differential protein expression associated with pancreas regeneration could be sought by 2-DE and mass spectroscopy and suggested that the pre-fractionation method combined with in vitro cell proliferation assay is effectively used to pinpoint the active components for pancreas regeneration.

Enhancement of radiosensitivity by combined ceramide and dimethylsphingosine treatment in lung cancer cells

Ceramide generated from sphingomyelin in response to ionizing radiation has been implicated as a second messenger to induce cellular proapoptotic signals. Both ceramide and its metabolic inhibitor, N, N-dimethyl-D-erythro-sphingosine (DMS), might lead to sustained ceramide accumulation in cells more efficiently, thereby sensitizing them to gamma-radiation-induced cell death. To delineate this problem, the clonogenic survival of Lewis lung carcinoma (LLC) cells was evaluated following exposure to radiation together with or without C2-ceramide, DMS, or both. The treatment of ceramide/DMS synergistically decreased the survival of the irradiated cells compared with treatment with ceramide or DMS alone. Ceramide/DMS-treated cells displayed several apoptotic features after gamma-irradiation, including increased sub G(1) population, TUNEL-positive fraction, and poly-(ADP-ribose) polymerase (PARP) cleavage. We also observed ceramide/ DMS induced disruption of mitochondrial membrane potential (MMP) and activation of caspase- 9 and -3 in a radiation-dose-dependent manner. Furthermore, pretreatment of LLC cells with ceramide/DMS not only increased the protein expression level of Bax, but also decreased Bcl-2 after gamma-irradiation. Taken together, the present study indicates that the radiosensitizing activity of ceramide/DMS on LLC cells most likely reflects the dominance of pro-apoptotic signals related to the mitochondria-dependent pathway.

Identification of a novel protein D3UPCA from Halobacterium salinarum and prediction of its function

Halobacterium salinarum is an extremely halophilic archaea, which is able to live in highly saline environments. In a recent study, several halophilic archaea were found to have the ability to biodegrade organic hydrocarbon pollutants, but protein information regarding hydrocarbon degradation and tolerance in halophilic archaea has been relatively rare. In this study, the protein expression profile of H. salinarum cultured under different diesel concentrations (0, 2 and 4%) was investigated by two-dimensional gel electrophoresis. Proteins which increased their expression levels in diesel media were identified using matrix-assisted laser desorption/ionization-time of flight and electrospray ionization-tandem mass spectrometry analysis. Among these, a protein spot (named D3UPCA) which was up-regulated about nine-fold and found to have COG3388, an uncharacterized protein conserved in archaea, was selected in order to further characterize its functions. The D3UPCA coding gene (named d3upca) was cloned and expressed in Escherichia coli, and purified by the glutathione-S-transferase-fusion method. The function of the protein was estimated using various bioinformatics tools and was predicted to be related to the regulation of transcription and/or translation of genes needed to tolerate stresses associated within the presence of diesel oil.

Quantitative profiling of plasma peptides in asthmatic mice using liquid chromatography and mass spectrometry

Asthma is increasing in prevalence worldwide as a result of factors associated with a Western lifestyle. However, simple and reliable diagnostic and prognostic markers are yet to be found. In an attempt to identify protein biomarker profiles among small molecular weight ranges, we employed an approach combining liquid chromatography with mass spectrometry, instead of two-dimensional gel electrophoresis (2-DE), which has previously been used to analyze protein expression patterns. Here we described its application to compare plasma peptides from control and chronic asthma mice. Peptides were quantitatively profiled as a multidimensional peptide mass fingerprint by a combination of reverse-phase high-performance liquid chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. They were identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry. In this study, we quantitatively identified the fragment f of complement 3 (C3f), which is important in inflammation. C3f was significantly higher in controls than chronic asthma mice. Our strategy allowed the detection and identification of different plasma peptides between control and chronic asthma mice on a proteomic scale. Therefore, these results suggest that native small peptides detected by non-2-DE techniques may be useful and specific biomarkers of disease.