Many cellular functions involve protein complexes that are formed by multiple interacting proteins. Tandem Affinity Purification (TAP) is a popular experimental method for detecting such multi-protein interactions. However, current computational methods that predict protein complexes from TAP data require converting the co-complex relationships in TAP data into binary interactions. The resulting pairwise protein-protein interaction (PPI) network is then mined for densely connected regions that are identified as putative protein complexes. Converting the TAP data into PPI data not only introduces errors but also loses useful information about the underlying multi-protein relationships that can be exploited to detect the internal organization (i.e., core-attachment structures) of protein complexes. In this article, we propose a method called CACHET that detects protein complexes with Core-AttaCHment structures directly from bipartitETAP data. CACHET models the TAP data as a bipartite graph in which the two vertex sets are the baits and the preys, respectively. The edges between the two vertex sets represent bait-prey relationships. CACHET first focuses on detecting high-quality protein-complex cores from the bipartite graph. To minimize the effects of false positive interactions, the bait-prey relationships are indexed with reliability scores. Only non-redundant, reliable bicliques computed from the TAP bipartite graph are regarded as protein-complex cores. CACHET constructs protein complexes by including attachment proteins into the cores. We applied CACHET on large-scale TAP datasets and found that CACHET outperformed existing methods in terms of prediction accuracy (i.e., F-measure and functional homogeneity of predicted complexes). In addition, the protein complexes predicted by CACHET are equipped with core-attachment structures that provide useful biological insights into the inherent functional organization of protein complexes. Our supplementary material can be found at
http://www1.i2r.a-star.edu.sg/∼xlli/CACHET/CACHET.htm; binary executables can also be found there. Supplementary Material is also available at
algorithms; gene clusters; gene networks
The development of diabetic angiopathy is associated with profound vascular endothelial cells (VEC) dysfunction and apoptosis. Glycated low density lipoproteins (gly-LDL) continuously produced in the setting of diabetic patients play an important role in causing VEC dysfunction and apoptosis. However, the underlying molecular mechanism remains largely elusive. Protein L-isoaspartyl methyltransferase (PIMT) is a widely expressed protein repair enzyme by multiple cell types of arterial wall including VEC. Our previous proteomic studies showed that the expression of PIMT was significantly decreased in the aorta of diabetic rats as compared with control rats and treatment with grape seed procyanidin extracts significantly increased the PIMT expression in diabetic rats. We hypothesized that PIMT plays a critical role in gly-LDL induced VEC apoptosis; grape seed procyanidin B2 (GSPB2) protect against gly-LDL induced VEC apoptosis through PIMT regulation.
Methods and Results
HUVEC transfected negative control and PIMT siRNA were treated with or without GSPB2 (10 µmol/L) for 48 h. Moreover, HUVEC of PIMT overexpression were stimulated by gly-LDL (50 µg/ml) in the presence or absence of GSPB2 (10 µmol/L) for 48 h. Our results showed that gly-LDL downregulated PIMT expression and PIMT overexpression or GSPB2 significantly attenuated gly-LDL induced VEC apoptosis. PIMT siRNA increased VEC apoptosis with up-regulation of p53, cytochrome c release, caspase-9 and caspase-3 activation. Mechanistically, overexpression of PIMT or GSPB2 increased the phosphorylation of ERK1/2 and GSK3β in the gly-LDL induced VEC.
In summary, our study identified PIMT as a key player responsible for gly-LDL induced VEC apoptosis and GSPB2 protect against gly-LDL induced VEC apoptosis by PIMT up-regulation. Targeting PIMT including use of GSPB2 could be turned into clinical application in the fighting against diabetic vascular complications.
The temperature and stress characteristic of photonic band gap structure resonant cavities with square and graphite lattice have been studied by finite-difference time-domain method. The results show that the resonant cavities, both square and graphite lattice, have more and more resonant frequency with the cavity enlarging. And the curves between the resonant frequency and stress have better linearity. When the cavity enlarges enough, the curve between resonant frequency and temperature will become sectionalized line from nonlinear curve. Especially, the temperature sensitivity will be descending as the cavity is enlarging. Nevertheless, once some structures are put in the center of the cavity, the temperature sensitivity will be rising fast for this kind of cavity. Obviously, this character is convenient for us to achieve the specification measurement for temperature and stress.
The present study aimed to investigate how ongoing brain rhythmical oscillations changed during the postoperative pain and whether electroacupuncture (EA) regulated these brain oscillations when it relieved pain. We established a postincisional pain model of rats with plantar incision to mimic the clinical pathological pain state, tested the analgesic effects of EA, and recorded electroencephalography (EEG) activities before and after the EA application. By analysis of power spectrum and bicoherence of EEG, we found that in rats with postincisional pain, ongoing activities at the delta-frequency band decreased, while activities at theta-, alpha-, and beta-frequency bands increased. EA treatment on these postincisional pain rats decreased the power at high-frequency bands especially at the beta-frequency band and reversed the enhancement of the cross-frequency coupling strength between the beta band and low-frequency bands. After searching for the PubMed, our study is the first time to describe that brain oscillations are correlated with the processing of spontaneous pain information in postincisional pain model of rats, and EA could regulate these brain rhythmical frequency oscillations, including the power and cross-frequency couplings.
To assess the prevalence of and related risk factors for aspirin resistance in elderly patients with coronary artery disease (CAD).
Two hundred and forty-six elderly patients (75.9 ± 7.4 years) with CAD who received daily aspirin therapy (≥ 75 mg) over one month were recruited. The effect of aspirin was assessed using light transmission aggregometry (LTA) and thrombelastography platelet mapping assay (TEG). Aspirin resistance was defined as ≥ 20% arachidonic acid (AA)-induced aggregation and ≥ 70% adenosine diphosphate (ADP)-induced aggregation in the LTA assay. An aspirin semi-responder was defined as meeting one (but not both) of the criteria described above. Based on the results of TEG, aspirin resistance was defined as ≥ 50% aggregation induced by AA.
As determined by LTA, 23 (9.3%) of the elderly CAD patients were resistant to aspirin therapy; 91 (37.0%) were semi-responders. As determined by TEG, 61 patients (24.8%) were aspirin resistant. Of the 61 patients who were aspirin resistant by TEG, 19 were aspirin resistant according to LTA results. Twenty-four of 91 semi-responders by LTA were aspirin resistant by TEG. Multivariate logistic regression analysis revealed that elevated fasting serum glucose level (Odds ratio: 1.517; 95% CI: 1.176–1.957; P = 0.001) was a significant risk factor for aspirin resistance as determined by TEG.
A significant number of elderly patients with CAD are resistant to aspirin therapy. Fasting blood glucose level is closely associated with aspirin resistance in elderly CAD patients.
Aspirin resistance; Coronary artery disease; Risk factors
Background: Identifying disease genes from human genome is an important but challenging task in biomedical research. Machine learning methods can be applied to discover new disease genes based on the known ones. Existing machine learning methods typically use the known disease genes as the positive training set P and the unknown genes as the negative training set N (non-disease gene set does not exist) to build classifiers to identify new disease genes from the unknown genes. However, such kind of classifiers is actually built from a noisy negative set N as there can be unknown disease genes in N itself. As a result, the classifiers do not perform as well as they could be.
Result: Instead of treating the unknown genes as negative examples in N, we treat them as an unlabeled set U. We design a novel positive-unlabeled (PU) learning algorithm PUDI (PU learning for disease gene identification) to build a classifier using P and U. We first partition U into four sets, namely, reliable negative set RN, likely positive set LP, likely negative set LN and weak negative set WN. The weighted support vector machines are then used to build a multi-level classifier based on the four training sets and positive training set P to identify disease genes. Our experimental results demonstrate that our proposed PUDI algorithm outperformed the existing methods significantly.
Conclusion: The proposed PUDI algorithm is able to identify disease genes more accurately by treating the unknown data more appropriately as unlabeled set U instead of negative set N. Given that many machine learning problems in biomedical research do involve positive and unlabeled data instead of negative data, it is possible that the machine learning methods for these problems can be further improved by adopting PU learning methods, as we have done here for disease gene identification.
Availability and implementation: The executable program and data are available at http://www1.i2r.a-star.edu.sg/∼xlli/PUDI/PUDI.html.
email@example.com or firstname.lastname@example.org
Supplementary Data are available at Bioinformatics online.
The management of ovarian cancer during pregnancy is still a big challenge, mostly due to the reciprocal impacts between cancer and pregnancy. The objective of this article is to present a rare case of maternal ovarian adenocarcinoma and review published similar cases about this clinical condition.
Materials and methods
Here we report a rare case of maternal ovarian adenocarcinoma detected during gestational week 6, with good pregnancy outcome treated with conservative surgery.
Results and discussion
A case of maternal ovarian adenocarcinoma (stage I) was detected in week 6 of pregnancy receiving conservative surgery without chemotherapy. In week 39 of pregnancy, due to relapse of the cancer, the patient underwent excision of the isolated tumor, and gave birth to a healthy baby through cesarian section. After that, the patient received cytoreductive surgery associated with six chemotherapy. The patient was finally diagnosed as epithelial ovarian cancer stage IIIC, and had survived more than 5 years without relapse. The successful experience from this case suggested that pregnancy complicated with early ovarian cancer receiving conservative surgery could continue to pregnancy and the effect of cesarian section followed with cytoreductive surgery associated with six chemotherapy at full term was still satisfied.
Pregnancy; Ovarian cancer; Cytoreductive surgery; Chemotherapy
Multidrug resistance (MDR) is the major obstacle in chemotherapy, which involves multiple signaling pathways. Diallyl trisulfide (DATS) is the main sulfuric compound in garlic. In the present study, we aimed to explore whether DATS could overcome P-glycoprotein-(P-gp-)mediated MDR in K562/A02 cells, and to investigate whether NF-κB suppression is involved in DATS-induced reversal of MDR. MTT assay revealed that cotreatment with DATS increased the response of K562/A02 cells to adriamycin (the resistance reversal fold was 3.79) without toxic side effects. DATS could enhance the intracellular concentration of adriamycin by inhibiting the function and expression of P-gp, as shown by flow cytometry, RT-PCR, and western blot. In addition, DATS resulted in more K562/A02 cell apoptosis, accompanied by increased expression of caspase-3. The expression of NF-κB/p65 (downregulation) was significantly linked to the drug-resistance mechanism of DATS, whereas the expression of IκBα was not affected by DATS. Our findings demonstrated that DATS can serve as a novel, nontoxic modulator of MDR, and can reverse the MDR of K562/A02 cells in vitro by increasing intracellular adriamycin concentration and inducing apoptosis. More importantly, we proved for the first time that the suppression of NF-κB possibly involves the molecular mechanism in the course of reversion by DATS.
The human papillomavirus (HPV) E2 protein is a multifunctional DNA-binding protein. The transcriptional activity of HPV E2 is mediated by binding to its specific binding sites in the upstream regulatory region of the HPV genomes. Previously we reported a HPV-2 variant from a verrucae vulgaris patient with huge extensive clustered cutaneous, which have five point mutations in its E2 ORF, L118S, S235P, Y287H, S293R and A338V. Under the control of HPV-2 LCR, co-expression of the mutated HPV E2 induced an increased activity on the viral early promoter. In the present study, a series of mammalian expression plasmids encoding E2 proteins with one to five amino acid (aa) substitutions for these mutations were constructed and transfected into HeLa, C33A and SiHa cells.
CAT expression assays indicated that the enhanced promoter activity was due to the co-expressions of the E2 constructs containing A338V mutation within the DNA-binding domain. Western blots analysis demonstrated that the transiently transfected E2 expressing plasmids, regardless of prototype or the A338V mutant, were continuously expressed in the cells. To study the effect of E2 mutations on its DNA-binding activity, a serial of recombinant E2 proteins with various lengths were expressed and purified. Electrophoresis mobility shift assays (EMSA) showed that the binding affinity of E2 protein with A338V mutation to both an artificial probe with two E2 binding sites or HPV-2 and HPV-16 promoter-proximal LCR sequences were significantly stronger than that of the HPV-2 prototype E2. Furthermore, co-expression of the construct containing A338V mutant exhibited increased activities on heterologous HPV-16 early promoter P97 than that of prototype E2.
These results suggest that the mutation from Ala to Val at aa 338 is critical for E2 DNA-binding and its transcriptional regulation.
HPV-2; E2; DNA-binding; Transcriptional regulation; Promoter
2009 pandemic H1N1 (pH1N1) influenza posed an increased risk of severe illness among pregnant women. Data on risk factors associated with death of pregnant women and neonates with pH1N1 infections are limited outside of developed countries.
Retrospective observational study in 394 severe or critical pregnant women admitted to a hospital with pH1N1 influenza from Sep. 1, 2009 to Dec. 31, 2009. rRT-PCR testing was used to confirm infection. In-hospital mortality was the primary endpoint of this study. Univariable logistic analysis and multivariate logistic regression analysis were used to investigate the potential factors on admission that might be associated with the maternal and neonatal mortality.
394 pregnant women were included, 286 were infected with pH1N1 in the third trimester. 351 had pneumonia, and 77 died. A PaO2/FiO2 ≤ 200 (odds ratio (OR), 27.16; 95% confidence interval (CI), 2.64-279.70) and higher BMI (i.e. ≥ 30) on admission (OR, 1.26; 95% CI, 1.09 to 1.47) were independent risk factors for maternal death. Of 211 deliveries, 146 neonates survived. Premature delivery (OR, 4.17; 95% CI, 1.19-14.56) was associated neonatal mortality. Among 186 patients who received mechanical ventilation, 83 patients were treated with non-invasive ventilation (NIV) and 38 were successful with NIV. The death rate was lower among patients who initially received NIV than those who were initially intubated (24/83, 28.9% vs 43/87, 49.4%; p = 0.006). Septic shock was an independent risk factor for failure of NIV.
Severe hypoxemia and higher BMI on admission were associated with adverse outcomes for pregnant women. Preterm delivery was a risk factor for neonatal death among pregnant women with pH1N1 influenza infection. NIV may be useful in selected pregnant women without septic shock.
Pregnant women; Neonate; Pandemic H1N1 influenza; Mortality; Non-invasive ventilation
There is limited data on the clinical outcome of patients with pandemic H1N1 (pH1N1) pneumonia who received oseltamivir treatment, especially when the treatment was administered more than 48 hours after symptom onset.
During the pandemic in 2009, a cohort of pH1N1 influenza pneumonia was built in China, and their clinical information was collected systematically, and analyzed with Cox models.
920 adults and 541 children with pneumonia who didn't receive corticosteroids were analyzed. In-hospital mortality was higher in adults who did not receive antiviral therapy (18.2%) than those with who received oseltamivir ≤ 2days (2.9%), between 2–5 days (4.6%) and >5 days after illness onset (4.9%), p<0.01. A similar trend was observed in pediatric patients. Cox regression showed that at 60 days after symptoms onset, 11 patients (10.8%) who did not receive antivirals died versus 4 (1.8%), 18 (3.3%), and 23 (3.7%) patients whose oseltamivir treatment was started ≤ 2days, between 2–5days, and >5 days, respectively. For males patients, aged ≥ 14 years and baseline PaO2/FiO2<200, oseltamivir administration reduced the mortality risk by 92.1%, 88% and 83.5%, respectively. Higher doses of oseltamivir (>3.8 mg/kg/d) did not improve clinical outcome (mortality, higher dose 2.5% vs standard dose 2.8%, p>0.05).
Antiviral therapy might reduce mortality of patients with pH1N1 pneumonia, even when initiated more than 48 hours after onset of illness. Greater protective effects might be in males, patients aged 14–60 years, and patients with PaO2/FiO2<200.
Motivation: Protein complexes are of great importance for unraveling the secrets of cellular organization and function. The AP-MS technique has provided an effective high-throughput screening to directly measure the co-complex relationship among multiple proteins, but its performance suffers from both false positives and false negatives. To computationally predict complexes from AP-MS data, most existing approaches either required the additional knowledge from known complexes (supervised learning), or had numerous parameters to tune.
Method: In this article, we propose a novel unsupervised approach, without relying on the knowledge of existing complexes. Our method probabilistically calculates the affinity between two proteins, where the affinity score is evaluated by a co-complexed score or C2S in brief. In particular, our method measures the log-likelihood ratio of two proteins being co-complexed to being drawn randomly, and we then predict protein complexes by applying hierarchical clustering algorithm on the C2S score matrix.
Results: Compared with existing approaches, our approach is computationally efficient and easy to implement. It has just one parameter to set and its value has little effect on the results. It can be applied to different species as long as the AP-MS data are available. Despite its simplicity, it is competitive or superior in performance over many aspects when compared with the state-of-the-art predictions performed by supervised or unsupervised approaches.
Availability: The predicted complex sets in this article are available in the Supplementary information or by sending email to email@example.com
Supplementary information: Supplementary data are available at Bioinformatics online.
In this study, we investigated the inhibitive effects of Oplopanax horridus extract (OhE) and its fractions (OhF1, OhF2, OhF3, OhF4 and OhF5) on the growth of human colorectal cancer cells and the possible mechanisms.
Materials and Methods
The anti-proliferative effects were evaluated by MTS cell proliferation assay. Apoptotic effects and cell cycle distribution were analyzed by flow cytometry after staining with Annexin V/PI or PI/RNase.
After treatment for 48 hr, OhE, OhF4 and OhF5 (10–100 μg/ml) inhibited proliferation of HCT-116, SW-480 and HT-29 cell lines. And cell growth decreased most with the treatment of OhF4. On the other hand, OhF1, OhF2 and OhF3 were not observed to have obvious suppressive effects on these cell lines at concentrations of 10–100 μg/ml. OhE, OhF4 and OhF5 (1–10 μg/ml) noticeably induced apoptosis time- and concentration-dependently compared to the control at the same time point. Treatement with OhE, OhF4 or OhF5 (1–10 μg/ml) for 24 hr distinctly induced the G2/M phase arrest of the cell cycle in a dose-dependent manner. The trend of increasing cyclin A and cyclin B1 were similar to the increase of G2/M phase cells in all treated groups.
These results showed that OhE had potential anti-proliferation effects on human colorectal cancer cells, and the active components were enriched in the fractions OhF4 and OhF5. The anticancer mechanism of OhE, OhF4 and OhF5 might be attributed to the induction of apoptotic cells and the regulation of cell cycle transition.
Oplopanax horridus; human colorectal cancer; anti-proliferation; apoptosis; cell cycle; cyclin A; cyclin B1
Oplopanax horridus is used as a folk medicine by natives in the Northern Pacific coast of North America. This experiment studied the anti-proliferative effects of the extract of O. horridus root bark and its fractions chromatographed from Dianion HP20 resin column with water, 30, 50, 70 and 100% ethanol on human breast cancer MCF-7 cells and non-small cell lung cancer (NSCLC) cells. The role of O. horridus in the cell cycle and apoptosis of MCF-7 cells was also investigated. The results showed that the 70% and 100% ethanol fractions demonstrated more potent anti-proliferative effects than the total extract on both cell lines. The anti-proliferative effects may result from the enrichment of active constituents detected by the HPLC. The IC50 of the total extract, 50, 70, and 100% ethanol fractions for anti-proliferation on MCF-7 cells were 248.4, 123.1, 44.0, and 31.5 μg/mL, respectively, and on NSCLC cells were 125.3, 271.1, 17.6, and 23.2 μg/mL, respectively. On the other hand, the water and 30% ethanol fractions significantly promoted cell proliferation on MCF-7 cells at concentrations > 100 μg/mL, suggesting that the hydrophilic fractions should be removed from the extract when used for cancer chemoprevention in order to achieve desirable activities. The effects of the total extract on cell cycle and apoptosis were similar to that of the 100% ethanol fraction because of the similarity of their chemical composition. At higher concentrations, the apoptotic effects of the 70% ethanol fraction are more significant. Data from this study suggested that the 70% and 100% ethanol fractions are active anti-proliferative fractions and that induction of apoptosis is the mechanism involved in the anti-proliferative effect observed.
Oplopanax horridus; anti-proliferative effect; human breast cancer MCF-7 cells; non-small cell lung cancer (NSCLC) cells; apoptosis; cell cycle
Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous tumor profiles challenge current machine learning methodologies for its small number of samples and large or even huge number of variables (genes). This naturally calls for the use of an effective feature selection in microarray data classification.
We propose a novel feature selection method: multi-resolution independent component analysis (MICA) for large-scale gene expression data. This method overcomes the weak points of the widely used transform-based feature selection methods such as principal component analysis (PCA), independent component analysis (ICA), and nonnegative matrix factorization (NMF) by avoiding their global feature-selection mechanism. In addition to demonstrating the effectiveness of the multi-resolution independent component analysis in meaningful biomarker discovery, we present a multi-resolution independent component analysis based support vector machines (MICA-SVM) and linear discriminant analysis (MICA-LDA) to attain high-performance classifications in low-dimensional spaces.
We have demonstrated the superiority and stability of our algorithms by performing comprehensive experimental comparisons with nine state-of-the-art algorithms on six high-dimensional heterogeneous profiles under cross validations. Our classification algorithms, especially, MICA-SVM, not only accomplish clinical or near-clinical level sensitivities and specificities, but also show strong performance stability over its peers in classification. Software that implements the major algorithm and data sets on which this paper focuses are freely available at https://sites.google.com/site/heyaumapbc2011/.
This work suggests a new direction to accelerate microarray technologies into a clinical routine through building a high-performance classifier to attain clinical-level sensitivities and specificities by treating an input profile as a ‘profile-biomarker’. The multi-resolution data analysis based redundant global feature suppressing and effective local feature extraction also have a positive impact on large scale ‘omics’ data mining.
Based on our previous observation, the whole Scutellaria baicalensis extract (SbE) did not show significant breast cancer cell inhibitory effect. In this study, we isolated a baicalin-deprived-fraction (SbF1) of Scutellaria baicalensis, and baicalin-fraction (SbF3), and evaluated their anti-breast cancer properties using MCF-7 cells. The content of four flavonoids in extract/fractions were determined using high performance liquid chromatography. Analytical data showed that in SbF1, the major constituents are baicalein and wogonin, while SbF3 only contains baicalin. The antiproliferative effects of fractions and SbE were assayed using modified trichrome stain method. SbF1 showed significant antiproliferative effect. Treated with 100 µg/ml of SbF1 for 72 h inhibited MCF-7 cell growth by 81.6%, while in the same treatment concentration, SbF3 increased cell growth by 22.6%. SbF1 was recognized as an active fraction of SbE. The effects of four flavonoids in SbE, scutellarin, baicalin, baicalein and wogonin, were determined, and data showed that baicalein and wogonin significantly inhibited MCF-7 cell growth. In contrast, in certain concentrations, scutellarin and baicalin increased cancer cell growth. The effects of SbF1 on cell cycle and apoptosis were assayed using flow cytometry. SbF1 arrested MCF-7 cells in S- and G2/M-phases, and significantly increased induction of cell apoptosis. These combined phytochemical and biological data provide evidence for further chemopreventive studies of the baicalin-deprived SbE on breast cancer.
Scutellaria baicalensis; Breast cancer; Apoptosis; Baicalin; Baicalein; Wogonin
To distinguish the extract of notoginseng root from that of other species in the genus Panax, we used reverse phase high performance liquid chromatography (HPLC) coupled with a principal component analysis (PCA) method. The content of 12 saponins in notoginseng root extracts from different sources was evaluated. Herbal extracts from different plant parts of notoginseng, Asian ginseng, and American ginseng were also evaluated. With an HPLC assay, however, it is difficult to determine whether notoginseng root extract has been adulterated with other plant parts or other Panax species before extraction. Therefore, we introduced PCA to identify adulteration in notoginseng root extract. PCA was performed on the data set obtained from the HPLC chromatogram. The HPLC-PCA assay not only distinguished notoginseng root extract from the extract of other plant parts of notoginseng, but also from the extract of Asian or American ginseng plant parts.
Panax notoginseng; extract authentication; adulteration; genus Panax; dammarane saponins; HPLC; PCA
Former studies have shown that extract from American ginseng (Panax quinquefolius) may possess certain antiproliferative effects on cancer cells. In this study, the chemical constituents of both untreated and heat-processed American ginseng and their antiproliferative activities on human breast cancer cells were evaluated.
Materials and Methods
American ginseng roots were steamed at 120°C for 1 h or 2 h. The major ginsenosides in the two steamed and in the unsteamed extracts were quantitatively determined using high performance liquid chromatography (HPLC). The antiproliferative activities of these extracts and individual ginsenosides on MCF-7 and MDA-MB-231 breast cancer cells were assayed using the MTS method. The effects of the extracts and the ginsenosides on the induction of cell apoptosis, the expression of cyclins A and D1, and cell cycle arrest were evaluated.
Compared to the untreated extract, heat-processing reduced the content of ginsenosides Rb1, Re, Rc and Rd, and increased the content of Rg2 and Rg3. After 2 h steaming, the percent content of ginsenoside Rg3 was increased from 0.06% to 5.9%. Compared to the unsteamed extract, the 2 h steamed extract significantly increased the antiproliferative activity and significantly reduced the number of viable cells. The steamed extract also significantly reduced the expression of cyclin A and cyclin D1. The cell cycle assay showed that the steamed extract and ginsenoside Rg3 arrested cancer cells in G1-phase.
Heat-processing of American ginseng root significantly increases antiproliferative activity and influences the cell cycle profile.
Panax quinquefolius L.; heat-processing; antiproliferation; human breast cancer; HPLC analysis; ginsenoside Rg3; apoptosis; cell cycle
Numerous effective anticancer drugs have been developed from botanical sources, and there remains a significant untapped resource in herbal medicines. In this study, we evaluated the chemical composition of extracts from American ginseng after steaming, the antiproliferative effects of the ginsenosides in the extracts on SW-480 human colorectal cancer cells, and their apoptotic mechanisms. American ginseng roots were steamed at 120°C for 2 or 4 h. Representative ginsenosides in the unsteamed and steamed extracts were determined using HPLC. The antiproliferative effects of the ginsenosides Rb1, Rg3 and Rh2 on SW-480 cells were determined by the MTS method. The effect of extract steamed for 4 h on apoptosis of SW-480 cell was assayed by flow cytometry after staining with annexin V/PI. The expression of 84 apoptotic-related genes, including TNF, mitochondria and p53 pathways, was determined using real-time quantitative PCR array analysis. The mitochondrial membrane potential (Δψm) was analyzed after staining with FC-1. Steaming of American ginseng increased Rg3 and Rh2 content and antiproliferative activity significantly. The quantitative PCR array data demonstrated that multiple genes in mitochondrial pathway are involved in American ginseng-induced apoptosis of SW-480 cells and the expression profiling was validated by the cellular functional assay. The mitochondrial pathway may play a key role in American ginseng-mediated cancer cell apoptosis.
panax quinquefolius; steaming; real-time PCR array; mitochondrial apoptotic pathway; human colorectal cancer
The objective of the present study was to compare the toxicity and availability of Fe(II) and Fe(III) to Caco-2 cells. Cellular damage was studied by measuring cell proliferation and lactate dehydrogenase (LDH) release. The activities of two major antioxidative enzymes [superoxide dismutase (SOD) and glutathione peroxidase (GPx)] and differentiation marker (alkaline phosphatase) were determined after the cells were exposed to different levels of iron salts. The cellular iron concentration was investigated to evaluate iron bioavailability. The results show that iron uptake of the cells treated with Fe(II) is significantly higher than that of the cells treated with Fe(III) (P<0.05). Fe(II) at a concentration >1.5 mmol/L was found to be more effective in reducing cellular viability than Fe(III). LDH release investigation suggests that Fe(II) can reduce stability of the cell membrane. The activities of SOD and GPx of the cells treated with Fe(II) were higher than those of the cells treated with Fe(III), although both of them increased with raising iron supply levels. The results indicate that both Fe(II) and Fe(III) could reduce the cellular antioxidase gene expression at high levels.
Iron availability; Caco-2 cells; Fe(II); Fe(III); Toxicity
Quantitative simultaneous monitoring of the expression levels of thousands of genes under various experimental conditions is now possible using microarray experiments. However, there are still gaps toward whole-genome functional annotation of genes using the gene expression data.
In this paper, we propose a novel technique called Fuzzy Nearest Clusters for genome-wide functional annotation of unclassified genes. The technique consists of two steps: an initial hierarchical clustering step to detect homogeneous co-expressed gene subgroups or clusters in each possibly heterogeneous functional class; followed by a classification step to predict the functional roles of the unclassified genes based on their corresponding similarities to the detected functional clusters.
Our experimental results with yeast gene expression data showed that the proposed method can accurately predict the genes' functions, even those with multiple functional roles, and the prediction performance is most independent of the underlying heterogeneity of the complex functional classes, as compared to the other conventional gene function prediction approaches.
Atherosclerosis is one of the major complications of type 2 diabetic patients (T2DM), leading to morbidity and mortality. Grape seed procyanidin B2 (GSPB2) has demonstrated protective effect against atherosclerosis, which is believed to be, at least in part, a result of its antioxidative effects. The aim of this study is to identify the target protein of GSPB2 responsible for the protective effect against atherosclerosis in patients with DM.
Methods and Results
GSPB2 (30 mg/kg body weight/day) were administrated to db/db mice for 10 weeks. Proteomics of the aorta extracts by iTRAQ analysis was obtained from db/db mice. The results showed that expression of 557 proteins were either up- or down-regulated in the aorta of diabetic mice. Among those proteins, 139 proteins were normalized by GSPB2 to the levels comparable to those in control mice. Among the proteins regulated by GSPB2, the milk fat globule epidermal growth factor-8 (MFG-E8) was found to be increased in serum level in T2DM patients; the serum level of MFG-E8 was positively correlated with carotid-femoral pulse wave velocity (CF-PWV). Inhibition of MFG-E8 by RNA interference significantly suppressed whereas exogenous recombinant MFG-E8 administration exacerbated atherogenesis the db/db mice. To gain more insights into the mechanism of action of MFG-E8, we investigated the effects of MFG-E8 on the signal pathway involving the extracellular signal-regulated kinase (ERK) and monocyte chemoattractant protein-1 (MCP-1). Treatment with recombinant MFG-E8 led to increased whereas inhibition of MFG-E8 to decreased expression of MCP-1 and phosphorylation of ERK1/2.
Our data suggests that MFG-E8 plays an important role in atherogenesis in diabetes through both ERK and MCP-1 signaling pathways. GSPB2, a well-studied antioxidant, significantly inhibited the arterial wall changes favoring atherogenesis in db/db mice by down-regulating MFG-E8 expression in aorta and its serum level. Measuring MFG-E8 serum level could be a useful clinical surrogate prognosticating atherogenesis in DM patients.
Information on the health-related quality of life (HRQoL) of patients with genital warts (GW) in populations in mainland China is still limited. The aim of the study was to use a generic instrument to measure the impact of genital warts on HRQoL in men and women in this setting.
A multi-centre hospital-based cross-sectional study across 18 centers in China was conducted to interview patients using the European quality of life-5 dimension (EQ-5D) instrument; respondents' demographic and clinical data were also collected.
A total of 1,358 GW patients (612 men, 746 women) were included in the analysis, with a mean age of 32.0 ± 10.6 years. 56.4% of the patients reported some problems in the dimension of Anxiety/Depression (highest), followed by Pain/Discomfort (24.7%) and Mobility (3.5%). The overall visual analogue scale (VAS) score of the study population was found to be 65.2 ± 22.0, and the EQ-5D index score was found to be 0.843 ± 0.129 using Japanese preference weights (the Chinese preference was unavailable yet). Patients with lower VAS means and EQ-5D index scores were more often female, living in urban area, and suffering multiple GW (all p values < 0.05), but the values did not differ notably by age (p values > 0.05).
The HRQoL of patients with GW was substantially lower, compared to a national representative general population in China (VAS = ~80); the findings of different subgroups are informative for future GW prevention and control efforts.
Genetic prion diseases are linked to point and inserted mutations in the prion protein (PrP) gene that are presumed to favor conversion of the cellular isoform of PrP (PrPC) to the pathogenic one (PrPSc). The pathogenic mechanisms and the subcellular sites of the conversion are not completely understood. Here we introduce several PRNP gene mutations (such as, PrP-KDEL, PrP-3AV, PrP-A117V, PrP-G114V, PrP-P102L and PrP-E200K) into the cultured cells in order to explore the pathogenic mechanism of familial prion disease.
To address the roles of aberrant retention of PrP in endoplasmic reticulum (ER), the recombinant plasmids expressing full-length human PrP tailed with an ER signal peptide at the COOH-terminal (PrP-KDEL) and PrP with three amino acids exchange in transmembrane region (PrP-3AV) were constructed. In the preparations of transient transfections, 18-kD COOH-terminal proteolytic resistant fragments (Ctm-PrP) were detected in the cells expressing PrP-KDEL and PrP-3AV. Analyses of the cell viabilities in the presences of tunicamycin and brefeldin A revealed that expressions of PrP-KDEL and PrP-3AV sensitized the transfected cells to ER stress stimuli. Western blots and RT-PCR identified the clear alternations of ER stress associated events in the cells expressing PrP-KDEL and PrP-3AV that induced ER mediated apoptosis by CHOP and capase-12 apoptosis pathway. Moreover, several familial CJD related PrP mutants were transiently introduced into the cultured cells. Only the mutants within the transmembrane region (G114V and A117V) induced the formation of Ctm-PrP and caused the ER stress, while the mutants outside the transmembrane region (P102L and E200K) failed.
The data indicate that the retention of PrP in ER through formation of Ctm-PrP results in ER stress and cell apoptosis. The cytopathic activities caused by different familial CJD associated PrP mutants may vary, among them the mutants within the transmembrane region undergo an ER-stress mediated cell apoptosis.
Phospho-tau deposition has been described in a rare genetic human prion disease, Gerstmann-Sträussler-Scheinker syndrome, but is not common neuropathological picture for other human and animal transmissible spongiform encephalopathies (TSEs). This study investigated the possible changes of tau and phosphorylated tau (p-tau, at Ser396, Ser404, and Ser202/Thr205) in scrapie experimental animals.
The profiles of tau and p-tau (p-tau, at Ser396, Ser404, and Ser202/Thr205) in the brain tissues of agents 263K- or 139A-infected hamsters were evaluated by Western blots and real-time PCR. Meanwhile, the transcriptional and expressive levels of GSK3β and CDK5 in the brains were tested.
The contents of total tau and p-tau at Ser202/Thr205 increased, but p-tau at Ser396 and Ser404 decreased at the terminal stages, regardless of scrapie strains. Transcriptional levels of two tau isoforms were also increased. Additionally, it showed higher CDK5, but lower GSK3β transcriptional and expressive levels in the brains of scrapie-infected animals. Analysis of brain samples collected from different times after inoculated with agent 263 K revealed that the changes of tau profiles and phosphate kinases were time-relative events.
These data suggest that changes of profiles of p-tau at Ser396, Ser404 and Ser202/Thr205 are illness-correlative phenomena in TSEs, which may arise of the alteration of phosphate kinases. Alteration of tau, p-tau (Ser396, Ser404, and Ser202/Thr205), GSK3β and CDK5 were either intermediate or consequent events in TSE pathogenesis and proposed the potential linkage of these bioactive proteins with the pathogenesis of prion diseases.