[Relationship between vitamin D receptor gene polymorphisms and gestational diabetes mellitus: a case-control study].

Objective: To investigate the relationship between vitamin D receptor (VDR) gene polymorphisms and gestational diabetes mellitus (GDM) and provide evidence for the study of the mechanism of GDM. Methods: A case-control study design was used to study pregnant women who delivered in the obstetrics department of the First Hospital of Shanxi Medical University from March 1, 2012 to July 30, 2014. Of these, 334 cases were diagnosed with GDM and were matched 1∶1 by age, gestation time and residence to corresponding healthy controls. DNA genotyping was performed for the study subjects, and those with genotyping deletions >10% were excluded. Finally 323 cases and 320 controls were included in the study. Under co-dominant, dominant, recessive, and allele genetic models, unconditional logistic regression analysis on the relationship between VDR gene locus polymorphism and GDM was conducted. And software Haploview was used to analyze the relationship between haplotype and GDM. Results: At the genetic level, VDR gene was associated with the risk of developing GDM (P<0.05). After adjusting for pre-pregnancy body mass index, family history of diabetes, it was found that rs7967152 loci was associated with an increased risk of developing GDM (AC vs. AA, OR=1.58, 95%CI: 1.13-2.21; AC+CC vs. AA, OR=1.58, 95%CI: 1.15-2.18; C vs. A, OR=1.41, 95%CI: 1.10-1.82) and rs2238140 loci was associated with an increased risk of developing GDM (AA vs. GG, OR=2.24, 95%CI: 1.19-4.20; GA+AA vs. GG, OR=1.48, 95%CI: 1.07-2.03; A vs. G, OR=1.43, 95%CI: 1.11-1.83). Carrying rs2853564 locus AG genotype and AG+GG genotype (OR=1.46, 95%CI: 1.04-2.05; OR=1.45, 95%CI: 1.05-2.00) compared with carrying AA genotype and carrying rs2853566 locus AG genotype and AG+GG genotype (OR=1.43, 95%CI: 1.03-2.00; OR=1.41, 95%CI: 1.02-1.94) compared with carrying AA genotype were risk factors for GDM. Haplotype block consisting of rs1544410, rs7967152 in the VDR gene with GC haplotype was a risk factor for GDM(OR=1.50, 95%CI: 1.15-1.97). Conclusions: VDR gene rs7967152, rs2238140, rs2853564, rs2853566 locus polymorphisms and block (rs1544410, rs7967152) GC haplotype were associated with an incrased risk of developing GDM.

[Relationship between the pre-pregnancy BMI, gestational weight gain, and risk of preeclampsia and its subtypes].

Objective: To explore the effects of maternal pre-pregnancy body mass index (BMI) and gestational weight gain and its subtypes on the risk of preeclampsia. Methods: Pregnant women delivered in the Department of Obstetrics and Gynecology of the First Affiliated Hospital of Shanxi Medical University from March 2012 to September 2016 were selected as the research subjects. According to the inclusion and exclusion criteria, 9 274 pregnant women were included. 901 preeclampsia pregnant women were selected as the case group, and 8 373 non-preeclampsia pregnant women were selected as the control group. General demographic characteristics, pre-pregnancy weight, height, lifestyle during pregnancy, reproductive history, and disease history of pregnant women were collected, and pre-pregnancy BMI and gestational weight gain were calculated. Unconditional logistic regression was used to analyze the relationship between pre-pregnancy BMI and weight gain during pregnancy and PE and its clinical subtypes. Results: Among the 901 preeclampsia after inclusion and exclusion, 401 cases were diagnosed as early-onset PE (EOPE), 500 cases were late-onset PE (LOPE), 178 cases were Mild PE (MPE), and 723 cases were severe PE (SPE). There were statistically significant differences between PE and non-PE pregnant women in terms of maternal age, residence, parity, family history of gestational diabetes and hypertension (P<0.05). After adjusting for the above factors, the logistic regression analysis results showed that pre-pregnancy BMI<18.5 kg/m2 and inadequate gestational weight gain were protective factors for PE (OR=0.74, 95%CI: 0.56-0.98; OR=0.78, 95%CI: 0.62-0.99), while pre-pregnancy BMI≥24.0 kg/m2 and excessive gestational weight gain were risk factors for PE (OR=1.82, 95%CI: 1.54-2.14; OR=1.82, 95%CI: 1.54-2.15). After subtype analysis on PE, the results showed that pre-pregnancy BMI<18.5 kg/m2 was a protective factor for EOPE and MPE (OR=0.52, 95%CI: 0.32-0.83; OR=0.47, 95%CI: 0.23-0.97), while pre-pregnancy BMI≥24.0 kg/m2 and excessive gestational weight gain were risk factors for clinical subtypes of PE. After stratification according to pre-pregnancy BMI, excessive gestational weight gain was the risk factor for PE (OR=1.86, 95%CI: 1.51-2.30; OR=1.90, 95%CI: 1.39-2.60) in pregnant women 18.5 kg/m2≤BMI<24.0 kg/m2 and ≥24.0 kg/m2. Inadequate gestational weight gain (OR=0.55, 95%CI: 0.34-0.89) was a protective factor for PE in pregnant women with pre-pregnancy BMI≥24.0 kg/m2. Excessive gestational weight gain (OR=4.05, 95%CI: 1.20-13.69) was a risk factor for EOPE in pregnant women with pre-pregnancy BMI<18.5 kg/m2. Excessive gestational weight gain was a risk factor for the clinical subtype of PE in pregnant women 18.5 kg/m2≤BMI<24.0 kg/m2 before pregnancy. Inadequate gestational weight gain was a protective factor for EOPE and MPE (OR=0.39, 95%CI: 0.19-0.80; OR=0.29, 95%CI: 0.11-0.77) in pregnant women with pre-pregnancy BMI≥24.0 kg/m2. Excessive weight gain was a risk factor for EOPE, LOPE and SPE (OR=1.60, 95%CI: 1.06-2.42;OR=2.20, 95%CI: 1.44-3.37;OR=2.28, 95%CI: 1.58-3.29). Conclusions: Pre-pregnancy BMI and gestational weight gain affect the risk of preeclampsia and its clinical subtypes. In contrast, the influence of gestational weight gain on preeclampsia varies among different pre-pregnancy BMI groups. Therefore, it is recommended to pay attention to the changes in pre-pregnancy BMI and gestational weight gain simultaneously to reduce preeclampsia.

A novel polysaccharide obtained from Craterellus cornucopioides enhances immunomodulatory activity in immunosuppressive mice models via regulation of the TLR4-NF-κB pathway.

The immunoregulatory effect of a novel Craterellus cornucopioides polysaccharide (CCP) with a triple-helix structure on immunosuppressive BALB/c mice models was investigated; moreover, the immune response of BALB/c mice models in the preventive and therapeutic treatment groups treated with CCP was explored, and its molecular mechanism was elucidated. It was found that the BALB/c mice models in the preventive groups treated with CCP (120 and 240 mg kg-1 d-1) had better immunoregulatory activity. The spleen and thymus weight indices of the BALB/c mice models were significantly increased, and the histopathological analysis indicated a protective function of CCP against the immunosuppression induced by cyclophosphamide (CTX). Moreover, CCP displayed definite and clear synergistic effects on the T- or B-lymphocyte proliferation induced by ConA or LPS, respectively, promoted the natural killer (NK) cell activity and significantly increased phagocytic activity to activate peritoneal macrophages in immunosuppressive mice. The western blot and quantitative real-time polymerase chain reaction (qRT-PCR) results provided comprehensive evidence that CCP could upregulate the protein expression of the G-protein-coupled cell membrane receptor TLR4 and the production of its downstream protein kinases (TRAF6, TK1, p-IKKα/ß and NF-κB p50); this, in turn, enhanced the production of cytokines (IL-2, IL-6, TNF-α and IFN-α) through both preventive and therapeutic treatments via regulation of the TLR4-NFκB pathway in the peritoneal macrophage of immunosuppressive mice.

[Effects of paraquat on the proliferation of human neural stem cells via DNA methylation].

Objective: To investigate the effects of Paraquat on neural stem cell proliferation in vitro and explore the its mechanism based on DNA methylation pathway. Methods: Nestin, ß-tubulin III, and glial fibrillary acidic protein (GFAP) were detected by indirect immunofluorescence assay to evaluate self renewal and differentiation potentia of ReNcell CX human neural stem. The cells were treated with terminal concentrations of 0, 5, 25, 50, and 100µmol/L PQ for 24 hours, and the cells were induced by 50 µmol/L PQ for different time (6, 12, 24, 48 h). Cell viability was determined by MTT assay. The proliferation of neural stem cells was evaluated using Sox2/Brdu and Nestin/Brdu double immunofluorescence staining. The global DNA methylation level was assayed by MethyflashTM methylated DNA Quantification kit. The expression levels of Dnmts mRNA and protein were analyzed by quantitative reverse transcription polymerase chain reaction(qRT-PCR) and Western blot, respectively. Results: Immunofluorescence showed that nestin was primarily expressed in proliferative neural stem cell and peotein biomarkers (ß-tubulin III, GFAP) for neuron and astrocyte were expressed in differentiated cells. MTT assay showed PQ induced cell survival rate decrease in a time and dose dependent manner. Double immunfluorescence staining of cells showed colocalization of Sox2 and Brdu. The percentage of Brdu/Sox2 positive cells was significantly lower in the PQ-exposed (25, 50, 100µmol/L PQ treatment) groups compared to control (P<0.05); Meanwhile, The percentage of Brdu/Nestin positive cells was also significantly lower in the PQ-exposed(50,100µmol/L PQ treatment) groups compared to control (P<0.05). The results of global DNA methylation revealed a significant decrease in PQ-exposed groups (P<0.05). Western blot showed that compared with control group, the protein and mRNA levels of Dnmt1, Dnmt3a in PQ-exposed group were significantly decreased (P<0.05), but there was a significant increase in expression level of Dnmt3b in 50, 100 µmol/L PQ-treated group(P<0.05). Conclusion: Paraquat could inhibite the proliferation of human neural stem cells through reducing the level of DNA methylation reaction by suppressing the protein expression and transcription of DNA methylated transferase(Dnmts).

Structure characterization, physicochemical property and immunomodulatory activity on RAW264.7 cells of a novel triple-helix polysaccharide from Craterellus cornucopioides.

In the study, a new triple-helix polysaccharide with favorable stability was purified from C. cornucopioides. Its structural characterization, stability and solution behavior were investigated by the GC-MS, periodate oxidation-smith degradation, FT-IR, 1D and 2D NMR spectroscopy, methylation analysis, Scanning electron microscope, Congo-red, CD, TGA and DSC analysis. The results showed that Craterellus cornucopioide polysaccharide (CCP) possessed the molecular weight of 1.97 × 103 kDa, is mainly composed of mannose (48.73%), galactose (17.37%), glucose (15.97%) and xylose (17.93%), respectively. It was a heteroglycan with (1 → 3)­linked­ß­d­Manp­(1 → 6)­linked α­d­Galp backbone distributed by (1 → 4)­linked­α­d­Xylp­t­α­d­Manp and t­ß­d­Glup units at O-6. The result of TGA and DSC assay indicated that CCP has a favorable thermal stability. MTT and Scanning electro microscopy (SEM) assay showed that CCP could significantly improve the proliferation activity and induce cells activation of RAW264.7 in a certain range of concentrations and period.

[Role of MAPK signaling pathway in epithelial-mesenchymal transition of type II alveolar epithelial cells induced by Paraquat].

Objective: To investigate the roles of p38 mitogen-activated protein kinases (p38 MAPK) , extracellular regulated protein kinases (ERK) and c-Jun N-tenninal kinases (JNK) of MAPK signaling pathway in Paraquat-induced epithelial to mesenchymal transition (EMT) of type II alveolarepithelial cells. Methods: RLE-6NT cells were incubated with different concentrations of PQ (0, 25, 50, 100µmol/L) for 6, 12 and 24 h. Cell morphology alteration was observed under phase-contrast microscopy. Cell viability was determined using an MTT assay. Cell migration ability was detected using scratch wound assay. Protein expression of P-p38 MAP, P-Erk1/2, P-JNK, E-cad, ZO-1, Vimentin and а-SMA were detected by western blot. The level of genes related to fibrosis (COL-I, COL-III, FN and FSP-1) were analyzed via quantitative real-time RT-PCR. Results: Cell morphology started to undergo EMT changes with a phenotype characteristic of mesenchymal cells, including an elongated shape and a lack of tight cell-cell adhesions induced by 100µmol/L PQ treatment in a time-dependent manner. MTT showed that cell viability decreased with increasing PQ concentration (50、100、200、300 µmol/L PQ treatment for 24 h) and increasing treatment time (200 µmol/L PQ treatment for 6, 12, 24, 36, 48 h) . Compared to control group, the expressions of the epithelial phenotype marker E-cad and ZO-1 significantly decreased with PQ treatment (50, 100µmol/L) in a time-dependent manner (P<0.05) . Additionally, the level of the mesenchymal marker (a-SMA, vimentin) dramatically increased with PQ treatment in the same concentration-and time-dependent manner (P<0.05) . Cell migration ability was markedly increased after 24 h of 100 µmol/L PQ treatment compared to control (P<0.05) . The phosphorylated forms of p38 MAPK, Erk1/2, and JNK were increased at 24 h after stimulation with PQ (P<0.05) . This PQ induced (100 µmol/L) phosphorylation was markedly attenuated in the presence of the p38 MAPK, ERK and JNK inhibitors (SB-203580, SP-600125 and PD98059) respectively. Furthermore, RT-PCR showed that PQ significantly induced the upregulation expression of COL I and III mRNA, Fn, and FSP-1 mRNA (P<0.05) . Conclusion: PQ-induced pulmonary fibrosis occurs via EMT, which is mediated by the MAPK pathway.

[The regulation of tight junction protein via PKCα/ß for abnormal permeability of brain microvascular endothelial cells exposed to paraquat].

Objective: To explore if conventional protein kinase C (cPKC: PKCα and PKCß) contributes to paraquat (PQ) -induced abnormal permeability of mouse brain microvascular endothelial cells (BMECs) via the regulation of tight junction (TJ) proteins. Methods: The immortalized mouse brain endothelial cell line (bEnd.3) was used to establish a monolayer blood-brain barrier (BBB) model. In order to evaluate the function of the in vitro BBB model, the transendothelial electrical resistance (TEER) and permeability were measured by a Millicell-ERS volt-ohmmeter and sodium fluorescent (Na-FLU) , respectively. MTT assay was used to determine the relative survival rate of cells. The dose-response relationship was determined by treating cells with 0, 50, 100, 200, and 300 µmol/L PQ for 24 hours. The time-response relationship was determined by treating cells with 200 µmol/L PQ for 6, 12, 24, 48, and 72 hours. After the treatment of cells with 0, 100, 200, and 300 µmol/L PQ for 24 hours, the protein and mRNA expression levels of ZO-1, Occludin, and Claudin-5 were measured by immunofluorescence (IF) and quantitative real-time RT-PCR (qRT-PCR) , respectively; the expression of PKCα, PKCß, phosphorylated (p) -PKCα, and p-PKCß was determined by Western blot. After the treatment of cells with 200? mol/L PQ for 24 hours following the pretreatment with a classical PKC inhibitor (Go 6983, 1 µmol/L) for 1 hour, the protein expression of ZO-1, Occludin, Claudin-5, p-PKCα, and p-PKCß was measured by Western blot. Results: The TEER of the bEnd. 3 cells increased gradually with the cell culture time, and reached a peak value of 114.3±6.9 Ω·cm(2) on day 6. According to the permeability analysis by Na-FLU, cell permeability gradually decreased with the cell culture time, and reached 1.7±0.2 cm/min on day 6, suggesting a well-behaved barrier function of cells. Compared with the control group, the survival rates of the bEnd.3 cells were significantly reduced after exposure to 100, 200, or 300 µmol/L PQ for 24 hours (P<0.05) , or after exposure to 200 µmol/L PQ for 6, 12, 24, 48, or 72 hours (P <0.05) , indicating a dose-and time-dependent relationship. The IF and qRT-PCR results showed that the protein and mRNA expression levels of ZO-1, Occludin, and Claudin-5 were significantly reduced with the increase in the concentration of PQ (P<0.05) . The Western blot analysis showed that compared with the control group, cells exposed to PQ had significantly higher protein expression of p-PKCα and p-PKCß and significantly lower protein expression of ZO-1, Occludin, and Claudin-5 (P<0.05) . Compared with the PQ treatment group, the Go 6983 intervention group had significantly higher protein expression of ZO-1, Occludin, and Claudin-5 and significantly lower protein expression of p-PKCα and p-PKCß (P<0.05) . Conclusion: By activation of cPKC (PKCα and PKCß) , PQ reduces the protein and mRNA expression of TJ proteins and enhances the permeability of murine BMECs.

imDC: an ensemble learning method for imbalanced classification with miRNA data.

Imbalances typically exist in bioinformatics and are also common in other areas. A drawback of traditional machine learning methods is the relatively little attention given to small sample classification. Thus, we developed imDC, which uses an ensemble learning concept in combination with weights and sample misclassification information to effectively classify imbalanced data. Our method showed better results when compared to other algorithms with UCI machine learning datasets and microRNA data.

FastJoin, an improved neighbor-joining algorithm.

Reconstructing the evolutionary history of a set of species is an elementary problem in biology, and methods for solving this problem are evaluated based on two characteristics: accuracy and efficiency. Neighbor-joining reconstructs phylogenetic trees by iteratively picking a pair of nodes to merge as a new node until only one node remains; due to its good accuracy and speed, it has been embraced by the phylogeny research community. With the advent of large amounts of data, improved fast and precise methods for reconstructing evolutionary trees have become necessary. We improved the neighbor-joining algorithm by iteratively picking two pairs of nodes and merging as two new nodes, until only one node remains. We found that another pair of true neighbors could be chosen to merge as a new node besides the pair of true neighbors chosen by the criterion of the neighbor-joining method, in each iteration of the clustering procedure for the purely additive tree. These new neighbors will be selected by another iteration of the neighbor-joining method, so that they provide an improved neighbor-joining algorithm, by iteratively picking two pairs of nodes to merge as two new nodes until only one node remains, constructing the same phylogenetic tree as the neighbor-joining algorithm for the same input data. By combining the improved neighbor-joining algorithm with styles upper bound computation optimization of RapidNJ and external storage of ERapidNJ methods, a new method of reconstructing phylogenetic trees, FastJoin, was proposed. Experiments with sets of data showed that this new neighbor-joining algorithm yields a significant speed-up compared to classic neighbor-joining, showing empirically that FastJoin is superior to almost all other neighbor-joining implementations.

Novel representation of RNA secondary structure used to improve prediction algorithms.

We propose a novel representation of RNA secondary structure for a quick comparison of different structures. Secondary structure was viewed as a set of stems and each stem was represented by two values according to its position. Using this representation, we improved the comparative sequence analysis method results and the minimum free-energy model. In the comparative sequence analysis method, a novel algorithm independent of multiple sequence alignment was developed to improve performance. When dealing with a single-RNA sequence, the minimum free-energy model is improved by combining it with RNA class information. Secondary structure prediction experiments were done on tRNA and RNAse P RNA; sensitivity and specificity were both improved. Furthermore, software programs were developed for non-commercial use.

Genetic algorithm-based efficient feature selection for classification of pre-miRNAs.

In order to classify the real/pseudo human precursor microRNA (pre-miRNAs) hairpins with ab initio methods, numerous features are extracted from the primary sequence and second structure of pre-miRNAs. However, they include some redundant and useless features. It is essential to select the most representative feature subset; this contributes to improving the classification accuracy. We propose a novel feature selection method based on a genetic algorithm, according to the characteristics of human pre-miRNAs. The information gain of a feature, the feature conservation relative to stem parts of pre-miRNA, and the redundancy among features are all considered. Feature conservation was introduced for the first time. Experimental results were validated by cross-validation using datasets composed of human real/pseudo pre-miRNAs. Compared with microPred, our classifier miPredGA, achieved more reliable sensitivity and specificity. The accuracy was improved nearly 12%. The feature selection algorithm is useful for constructing more efficient classifiers for identification of real human pre-miRNAs from pseudo hairpins.

Mining SNPs from EST sequences using filters and ensemble classifiers.

Abundant single nucleotide polymorphisms (SNPs) provide the most complete information for genome-wide association studies. However, due to the bottleneck of manual discovery of putative SNPs and the inaccessibility of the original sequencing reads, it is essential to develop a more efficient and accurate computational method for automated SNP detection. We propose a novel computational method to rapidly find true SNPs in public-available EST (expressed sequence tag) databases; this method is implemented as SNPDigger. EST sequences are clustered and aligned. SNP candidates are then obtained according to a measure of redundant frequency. Several new informative biological features, such as the structural neighbor profiles and the physical position of the SNP, were extracted from EST sequences, and the effectiveness of these features was demonstrated. An ensemble classifier, which employs a carefully selected feature set, was included for the imbalanced training data. The sensitivity and specificity of our method both exceeded 80% for human genetic data in the cross validation. Our method enables detection of SNPs from the user's own EST dataset and can be used on species for which there is no genome data. Our tests showed that this method can effectively guide SNP discovery in ESTs and will be useful to avoid and save the cost of biological analyses.

The mechanical and biological properties of demineralised cortical bone allografts in animals.

We studied the calcium content and mechanical strength of cortical bone from rats and dogs after different periods of demineralisation, showing that the rate of demineralisation differed considerably between the species. Specimens from the rat were further treated by chemical extraction and autolysis and tested for osteoinductive properties. We showed that partially demineralised cortical bone retained adequate mechanical strength, while retaining the biological effects of completely demineralised bone. This shows that it is possible to prepare allografts which have adequate mechanical strength and still retain osteo-inductive properties.

Design and application study of cell microcapsulation instrument.

This paper describes a device designed for controlling the size of cell-enveloping microcapsules. Microcapsule size varied inversely with air flow rate; an empirical formula was obtained relating packing density to microcapsule diameter. Microcapsule loading and cell distribution in the microcapsule are discussed. Finally, choice of microcapsule size is assessed, showing that smaller microcapsules result in better clone development.