Bio-Medical Materials and Engineering - Volume 26, issue s1

Authors: Li, Jin | Wang, Ying | Wang, Lei | Liang, Hong | Feng, Weixing | Meng, Xianglian | Cong, Wang | Liu, Yunlong

Article Type: Research Article

Abstract: Rifampin is an important drug used in the treatment of tuberculosis, and it increases the drug metabolism in human hepatocytes. Previous studies have shown that rifampin can indirectly influence drug deposition through the regulation of molecular interactions of miRNA, PXR and other genes. The potential functions of miRNAs associated with rifampin- induced drug disposition are poorly understood. In this study, significantly differentially expressed miRNAs (SDEM) were extracted and used to predict the miRNA-regulated co-expression target genes (MCeTG). Additionally, a miRNA-regulated co-expressed protein interaction network (MCePIN) was constructed for SDEM by extending from the protein interaction network (PIN). The functioning of …the miRNAs were analyzed using GO analysis and KEGG pathway enrichment analysis. A total of 20 miRNAs belonging to SDEM were identified, and 632 miRNA-regulated genes were predicted. The MCePIN was constructed by extending from PIN, and 10 miRNAs and 33 genes that are relevant to 7 functions, including response to wounding, wound healing, response to drug, defense response, inflammatory response, liver development and drug metabolism, were discerned. The results provided by this study offer valuable insights into the effect of rifampin on miRNAs, genes and protein levels. Show more

Keywords: Rifampin, miRNA, gene, hepatocyte, PPI network, P450

DOI: 10.3233/BME-151502

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1985-S1991, 2015

Authors: Kim, Yong-Hyuk | Yoon, Yourim

Article Type: Research Article

Abstract: We present a new genetic filter to identify a predictive gene subset for cancer-type classification on gene expression profiles. This approach pursues to not only maximize correlation between selected genes and cancer types but also minimize inter-correlation among selected genes. The proposed genetic filter was tested on well-known leukemia datasets, and significant improvement over previous work was obtained.

Keywords: Gene selection, filter method, genetic algorithm, cancer classification, gene expression data

DOI: 10.3233/BME-151503

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1993-S2002, 2015

Authors: Zhao, Qing | Wang, Dong | Chen, Yuehui | Qu, Xumi

Article Type: Research Article

Abstract: Protein subcellular localization prediction is currently receiving much attention in the field of protein research. Many researchers make great efforts to study single-site protein subcellular localization, but the experimental data shows that many proteins can be found in two or more sub-cellular locations, prompting the study of multisite protein sub-cellular localization. This study utilized a Gpos-mPLOC data set and pseudo amino acid compositions, physicochemical properties of amino acid composition, and entropy density as three effective feature extraction methods. Then, these features were then placed in a multi-label k nearest neighbor classifier to predict subcellular protein locations. Experimental results verified that …this approach provides a localization precision of 66.73% through the Jack-knife test. Show more

Keywords: Multisite, pseudo amino acid composition, physicochemical propertiess, entropy density, multi-label k nearest neighbor

DOI: 10.3233/BME-151504

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2003-S2009, 2015

Authors: Sun, Lin | Xu, Jiucheng | Yin, Ying

Article Type: Research Article

Abstract: One of the important problems in microarray gene expression data is tumor classification. This paper proposes a new feature selection method for tumor classification using gene expression data. In this method, three dimensionality reduction methods, including principal component analysis (PCA), factor analysis (FA) and independent component analysis (ICA), are first introduced to extract and select features for tumor classification, and their corresponding specific steps are given respectively. Then, the superiority of three algorithms is demonstrated by performing experimental comparisons on acute leukemia data sets. It is concluded that PCA compared with FA and ICA is the best under feature load …ratio. However, PCA cannot make full use of the category information. To overcome the weak point, Fisher linear discriminant (FLD) is employed as those components of PCA, and a new approach to principal component discriminant analysis (PCDA) is proposed to retain all assets and work better than both PCA and FLD for classification. The further experimental results show that the classification ability of selected feature subsets by means of PCDA is higher than that of the other related dimensionality reduction methods, and the proposed algorithm is efficient and feasible for tumor classification. Show more

Keywords: Feature selection, principal component, discriminant analysis, classification

DOI: 10.3233/BME-151505

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2011-S2017, 2015

Authors: Zhan, Yiling | Guo, Shuyuan

Article Type: Research Article

Abstract: Bacillus thuringiensis (Bt) is capable of producing a chitin-binding protein believed to be functionally important to bacteria during the stationary phase of its growth cycle. In this paper, the chitin-binding domain 3 protein HD73_3189 from B. thuringiensis has been analyzed by computer technology. Primary and secondary structural analyses demonstrated that HD73_3189 is negatively charged and contains several α -helices, aperiodical coils and β -strands. Domain and motif analyses revealed that HD73_3189 contains a signal peptide, an N-terminal chitin binding 3 domains, two copies of a fibronectin-like domain 3 and a C-terminal carbohydrate binding domain classified as CBM_5_12. Moreover, …analysis predicted the protein’s associated localization site to be the cell wall. Ligand site prediction determined that amino acid residues GLU-312, TRP-334, ILE-341 and VAL-382 exposed on the surface of the target protein exhibit polar interactions with the substrate. Show more

Keywords: Bacillus thuringiensis, chitin binding domain 3 protein, 3D structure, functional analysis

DOI: 10.3233/BME-151506

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2019-S2024, 2015

Authors: Huynh, Hieu Trung | Won, Yonggwan | Kim, Jinsul

Article Type: Research Article

Abstract: Hematocrit is a blood test that is defined as the volume percentage of red blood cells in the whole blood. It is one of the important indicators for clinical decision making and the most effective factor in glucose measurement using handheld devices. In this paper, a method for hematocrit estimation that is based upon the transduced current curve and the neural network is presented. The salient points of this method are that (1) the neural network is trained by the online sequential extreme learning machine (OS-ELM) in which the devices can be still trained with new samples during the using …process and (2) the extended features are used to reduce the number of current points which can save the battery power of devices and speed up the measurement process. Show more

Keywords: hematocrit, extreme learning machine, online training, OS-ELM, neural network

DOI: 10.3233/BME-151507

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2025-S2032, 2015

Authors: Xiao, Ting | Zeng, Ou | Luo, Jian | Wu, Zhixiong | Li, Fang | Yang, Jun

Article Type: Research Article

Abstract: In order to explore the effects of hydrogen sulfide (H2 S) on myocardial fibrosis in diabetic rats and its underlying mechanisms, intraperitoneal injections of streptozotocin were used to establish the diabetes models and sodium hydrosulfide (NaHS) was used as an exogenous donor of H2 S. Eight weeks later, Van Gieson staining was used to observe pathological changes, and basic hydrolysis methods were adopted to measure hydroxyproline content, while Western Blot was used to determine the expression of MMP2, MMP7, MMP11, MMP13, MMP16, TIMP1 and TGFβ 1.The results showed that significant myocardial fibrosis, decreased TIMP1 and MMP2 expression and increased MMP7, …MMP11, MMP13, MMP16 expressions occurred in diabetic group, but all these changes were significantly reversed in diabetic rats after NaHS treatment. This suggests that H2 S could attenuate cardiac fibrosis induced by diabetes and its mechanisms may be related to its modulation of MMPs/TIMPs expression and regulation of TGFβ 1. Show more

Keywords: Hydrogen sulfide, diabetic myocardial fibrosis, matrix metalloproteinases, tissue inhibitors of metalloproteinases, transforming growth factor beta1

DOI: 10.3233/BME-151508

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2033-S2039, 2015

Authors: Liu, Junli | Si, Shaoyan | Qin, Yaya | Zhang, Bin | Song, Shujun | Guo, Yanchuan

Article Type: Research Article

Abstract: Our study aimed at investigating the effect of different molecular weight bovine collagen peptides, namely CH878, CH1370, CH2900, and CH7747 on the differentiation of MC3T3-E1 cells. Osteogenic differentiation of MC3T3-E1 cells was assessed by a series of specific assays, after culturing of cells in the presence of collagen peptides. Alkaline phosphatase activity (ALP) was evaluated by NBT/BCIP staining. Osteocalcin expression was determined by a radioimmunology method. Mineralization was quantified by Alizarin Red staining. ALP staining results demonstrated that the ALP staining of cells after culture in the presence of collagen peptides were significantly higher than the control group (P<0.05), indicating …the promotion of ALP activity in MC3T3-E1 cells by these peptides. Radioimmunology results demonstrated that collagen peptides groups were all significantly higher than the control group (P<0.01). Alizarin Red staining results demonstrated that CH1370, CH2900, and CH7747 significantly promoted the formation of mineralized bone matrix. We therefore conclude that CH1370, CH2900, and CH7747 play an active role in the differentiation of MC3T3-E1 cells. Based on the above results, we provide molecular basis for further development of collagens with different molecular weight for the prevention and treatment of osteoporosis. Show more

Keywords: Different molecular weight collagen peptides, MC3T3-E1 cells, differentiation

DOI: 10.3233/BME-151509

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2041-S2047, 2015

Authors: Su, Yan | Han, Lisha | Gao, Lijun | Guo, Jun | Sun, Xiaorong | Li, Jiaxin | Qin, Wenbin

Article Type: Research Article

Abstract: In this paper, the hemoglobin (Hb) re-released from red blood cells (RBCs) and whole blood of 7 carcinoma patients were studied by using electrophoresis release test (ERT), which was established by our lab. Among the 7 carcinoma patients, the re-released Hb was distinctively increased from an intrahepatic bile duct carcinoma patient during one-dimension isotonic ERT. Different from the others, the result of double-dimension Hb re-release of this intrahepatic bile duct carcinoma patient showed that not only HbA but also HbA2 could be re-released from both RBCs and whole blood. The result of isotonic & hypotonic ERT which was performed …at room temperature showed that more Hb could be re-released from both RBCs and whole blood of the intrahepatic bile duct carcinoma patient than that of the normal control. After keeping the samples at 37°C for 1 hour, the re-released Hb from RBCs could still be found more than that of the normal control, but was disappeared completely from the whole blood sample. To our surprise, when the isotonic & hypotonic ERT was repeated 2 days later at 37°C, the re-released Hb from RBCs of the intrahepatic bile duct carcinoma patient was increased only in tube 4-6, and disappeared in the other tube. Further mechanism research work cannot be continued because of the patient’s leave, but ERT is speculated to be a useful and effective technology to observe the physiological or pathological change of RBCs, blood or body in the future. Show more

Keywords: Hemoglobin, red blood cell, electrophoresis release test, intrahepatic bile duct carcinoma

DOI: 10.3233/BME-151510

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2049-S2054, 2015

Authors: Yin, Kun | Zhao, Guihua | Huang, Xiaodan | Gao, Ge | Sun, Hui | Wei, Qingkuan | Liu, Qiaoqiao | Li, Mian | Xu, Chao | Zhu, Song | Ba, Zaihua | Yan, Ge

Article Type: Research Article

Abstract: Tumor necrosis factor-alpha (TNF-α ) has been used as an effective treatment for Hepatocellular Carcinoma, however, inducing tumor cell apoptosis by TNF-α alone is still unsatisfactory. RhoA is highly expressed in hepatocarcinoma cells and can be activated by TNF-α . The activation of RhoA directly leads to a poor prognosis of HCC. Therefore, we propose to investigate the therapeutic effect of TNF-α together with RhoA siRNA. RhoA inhibition was accomplished by constructing a recombinant adenovirus that can efficiently express RhoA siRNA in HepG2 cells. The recombinant adenovirus AdshRNA-RhoA and AdU6-control were generated by adenovirus-mediated siRNA expression system. The …inhibition effects were detected by RT-PCR in addition to immunoblot to quantify the decreased levels of RhoA expression, and the therapeutic effect for HCC was demonstrated by the proliferation and apoptosis ratios of HepG2 cells. The inhibition effects of RhoA by AdshRNA-RhoA were significant at both mRNA and protein levels: the transcription of RhoA mRNA decreased by 74.46%, and the expression of protein decreased by 76.48%. The proliferation rate of HepG2 cells detected by MTT showed that a treatment of AdshRNA-RhoA and TNF-α together could strengthen the suppression ability of TNF-α to HepG2 cells, resulting in approximately 14.2% more than those treated with only TNF-α . FCA and TUNEL assays results revealed that the combined treatment can induce apoptosis in approximately 52.14%-65% of the HepG2 cells, whereas this ratio in the TNF-α -alone group was only 21.91%-32%. Our results showed that AdshRNA-RhoA can efficiently enhance the TNF-α -induced apoptosis of hepatocarcinoma cells. This method might be a useful therapeutic route in HCC and other tumors. Show more

Keywords: RhoA, tumor necrosis factor-alpha, adenovirus-mediated siRNA, hepatocarcinoma cells, apoptosis

DOI: 10.3233/BME-151511

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S2055-S2067, 2015