Database and Tools for Metabolic Network Analysis

Lu Shi Jing,Farah Fathiah Muzaffar Shah,Mohd Saberi Mohamad,Nur Laily Hamran,Abdul Hakim Mohamed Salleh,Safaai Deris,Hany Alashwal 한국생물공학회 2014 Biotechnology and Bioprocess Engineering Vol.19 No.4

Metabolic network analysis has attracted muchattention in the area of systems biology. It has a profoundrole in understanding the key features of organismmetabolic networks and has been successfully applied inseveral fields of systems biology, including in silico geneknockouts, production yield improvement using engineeredmicrobial strains, drug target identification, and phenotypeprediction. A variety of metabolic network databases andtools have been developed in order to assist research inthese fields. Databases that comprise biochemical data arenormally integrated with the use of metabolic networkanalysis tools in order to give a more comprehensive result. This paper reviews and compares eight databases as wellas twenty one recent tools. The aim of this review is tostudy the different types of tools in terms of the featuresand usability, as well as the databases in terms of the scopeand data provided. These tools can be categorised intothree main types: standalone tools; toolbox-based tools;and web-based tools. Furthermore, comparisons of thedatabases as well as the tools are also provided to helpsoftware developers and users gain a clearer insight and abetter understanding of metabolic network analysis. Additionally, this review also helps to provide usefulinformation that can be used as guidance in choosing toolsand databases for a particular research interest.

Trajectory Linearization Based Output Tracking Control of an Unmanned Tandem Helicopter with Variance Constraints

Shi-Qian Liu,Zhong-Liang Jing,Jun-Guo Lu 제어·로봇·시스템학회 2010 International Journal of Control, Automation, and Vol.8 No.6

An output tracking control problem for an unmanned tandem rotor helicopter with variance constraints is investigated in this paper. A modified Trajectory Linearization Control (TLC) is proposed to stabilize a nonlinear continuous-time flight dynamics system of the tandem helicopter. The tracking controller structure of TLC is designed by using two-time-scale nonlinear dynamic inversion. The base control law of the translational and attitude loops is designed in a pseudo-inversion feedforward con-troller to deal with nonlinear features of the plant and a proportional integral controller to stabilize the linear slowly time-variant error system resulted from the nonlinear flight system. Furthermore, a feasi-ble TLC strategy is designed to meet a performance index set including steady trajectory tracking error variance and desired Parallel D-spectrum (PD-) eigenvalues to achieve good flight quality. The Vari-ance-constrained Trajectory Linearization Control (VCTLC) is designed to realize the desired steady tracking precision and agile capability. Flight simulation results show the VCTLC method is feasible and effective in attitude and altitude tracking.

Depression and Structural Factors Are Associated With Symptoms in Patients of Irritable Bowel Syndrome With Diarrhea

( Jia Lu ),( Lili Shi ),( Dan Huang ),( Wenjuan Fan ),( Xiaoqing Li ),( Liming Zhu ),( Jing Wei ),( Xiucai Fang ) 대한소화기기능성질환·운동학회(구 대한소화관운동학회) 2020 Journal of Neurogastroenterology and Motility (JNM Vol.26 No.4

Background/Aims A strong correlation between depression and irritable bowel syndrome with diarrhea (IBS-D) has been identified. The aim of this study is to identify the correlations among depression, structural factors, gastrointestinal (GI) and extra-GI symptoms, and efficacy of neuromodulators in patients with IBS-D. Methods Patients meeting the Rome III Diagnostic Criteria for IBS-D were enrolled. The intestinal symptoms and psychological states were evaluated using IBS-specific symptom questionnaires and Hamilton Depression Rating Scale. Results In total, 410 patients with IBS-D were enrolled, 28.8% (118/410) had comorbid depression. Patients with depression did not readily experience improvement in abdominal pain/discomfort after defecation, and had a higher prevalence of passing mucus, overlapping functional dyspepsia, and extra-GI symptoms. The structural factor “mental disorders” significantly correlated with main bowel symptom score and degree of pre-defecation abdominal pain/discomfort. No structural factor significantly correlated with bowel movements or stool form. Patients who had passing mucus, overlapping functional dyspepsia and extra-GI painful symptoms have higher score of “anxiety/somatization.” Patients with sexual dysfunction have higher score of “retardation symptoms.” In total, 28.3% of patients with IBS-D were prescribed neuromodulators. Baseline scores of “anxiety/somatization” and “retardation symptoms” positively correlated with improvement of diarrhea after paroxetine, and “sleep disturbances” positively correlated with improvement of abdominal pain/discomfort and diarrhea after mirtazapine. Conclusions Comorbid depression and higher scores of structural factors might aggravate GI and extra-GI symptoms other than bowel movements and stool form. Structural factors of Hamilton Depression Rating Scale correlated with efficacy of paroxetine and mirtazapine in patients with IBS-D. (J Neurogastroenterol Motil 2020;26:505-513)

Ginsenoside compound K protects against cerebral ischemia/ reperfusion injury via Mul1/Mfn2-mediated mitochondrial dynamics and bioenergy

Qingxia Huang,Jing Li,Jinjin Chen,Zepeng Zhang,Peng Xu,Hongyu Qi,Zhaoqiang Chen,Jiaqi Liu,Jing Lu,Mengqi Shi,Yibin Zhang,Ying Ma,Daqing Zhao,Xiangyan Li The Korean Society of Ginseng 2023 Journal of Ginseng Research Vol.47 No.3

Background: Ginsenoside compound K (CK), the main active metabolite in Panax ginseng, has shown good safety and bioavailability in clinical trials and exerts neuroprotective effects in cerebral ischemic stroke. However, its potential role in the prevention of cerebral ischemia/reperfusion (I/R) injury remains unclear. Our study aimed to investigate the molecular mechanism of ginsenoside CK against cerebral I/R injury. Methods: We used a combination of in vitro and in vivo models, including oxygen and glucose deprivation/reperfusion induced PC12 cell model and middle cerebral artery occlusion/reperfusion induced rat model, to mimic I/R injury. Intracellular oxygen consumption and extracellular acidification rate were analyzed by Seahorse multifunctional energy metabolism system; ATP production was detected by luciferase method. The number and size of mitochondria were analyzed by transmission electron microscopy and MitoTracker probe combined with confocal laser microscopy. The potential mechanisms of ginsenoside CK on mitochondrial dynamics and bioenergy were evaluated by RNA interference, pharmacological antagonism combined with co-immunoprecipitation analysis and phenotypic analysis. Results: Ginsenoside CK pretreatment could attenuate mitochondrial translocation of DRP1, mitophagy, mitochondrial apoptosis, and neuronal bioenergy imbalance against cerebral I/R injury in both in vitro and in vivo models. Our data also confirmed that ginsenoside CK administration could reduce the binding affinity of Mul1 and Mfn2 to inhibit the ubiquitination and degradation of Mfn2, thereby elevating the protein level of Mfn2 in cerebral I/R injury. Conclusion: These data provide evidence that ginsenoside CK may be a promising therapeutic agent against cerebral I/R injury via Mul1/Mfn2 mediated mitochondrial dynamics and bioenergy.

Temperature monitoring and analysis of a long-span cable-stayed bridge during construction period

Mei, Xiudao,Lu, Yiyan,Shi, Jing Techno-Press 2021 Structural monitoring and maintenance Vol.8 No.2

The temperature induced response of long-span cable-stayed bridge in cantilever state is significant, which is of great interest to study the temperature characteristics during construction period. A method of analyzing the eigenvalue and its extremum of daily temperature based on cubic spline function (CSF) is proposed. By setting the fixed time interval reasonably, introducing variable time interval and extracting nodes at the MinMax of daily temperature, the obtained CSF can approach the measured temperature curve with high accuracy. Based on CSF, the temperature characteristics at three levels of measuring point, section and component are analyzed in turn. The temperature monitoring data of a cable-stayed bridge with main span of 938 m and side span of steel-concrete composited box girder (CBG) during construction are analyzed. The results show that the temperature variation of steel box girder is remarkable; the steel beam of CBG is similar to steel box girder before composited, and it turns stable after composited; the influence of PE color on cable temperature is notable than that of the cable specification; as blue PE cable, the temperature difference of cable vs pylon and cable vs CBG exceed 17℃ and 13℃.

Coordinated Direct and Relayed Transmission based on NOMA and Backscattering

Zhaoxi Fang,Yingzhi Lu,Jing Zhou,Qi Li,Haiyan Shi 한국인터넷정보학회 2022 KSII Transactions on Internet and Information Syst Vol.16 No.9

We propose a spectral-efficient coordinated direct and relayed transmission (CDRT) scheme for a relay-assisted downlink system with two users. The proposed scheme is based on backscatter communication (BC) and non-orthogonal multiple access (NOMA) technique. With the proposed BC-NOMA-CDRT scheme, both users can receive one packet within one time slot. In contrast, in existing NOMA-CDRT schemes, the far user is only able to receive one packet in two time slots due to the half-duplex operation of the relay. We investigate the outage of the BC-NOMA-CDRT scheme, and derive the outage probability expressions in closed-form based on Gamma distribution approximation and Gaussian approximation. Numerical results show that the analytical results are accurate and the BC-NOMA-CDRT scheme outperforms the conventional NOMA-CDRT significantly.

Mesenchymal Stem Cells on a Decellularized Cartilage Matrix for Cartilage Tissue Engineering

Xi-Fu Zheng,Shi-Bi Lu,Wei-Guo Zhang,Shu-Yun Liu,Jing-Xiang Huang,Quan-Yi Guo 한국생물공학회 2011 Biotechnology and Bioprocess Engineering Vol.16 No.3

An ideal scaffold for cartilage tissue engineering should be biomimetic in not only its biochemical composition, but also in the morphological structure of the scaffold. In this study, we fabricated a scaffold with an oriented structure using a nanofibrous articular cartilage extracellular matrix (ACECM), in which the ACECM was used to mimic the biochemical composition and oriented structure of articular cartilage. Histology analysis showed that the scaffold contained cartilage ECM (GAGs and collagen II). Scanning electron microscopy (SEM) indicated that the scaffolds were composed of nanofibers and possessed vertical microtubules. Chondrogenic differentiation-induced mesenchymal stem cells (MSCs) were seeded on the scaffold in vitro. SEM showed that MSCs proliferated well and aligned along the vertical microtubules,which mimicked the orientation of deep zone articular cartilage. A cell proliferation assay and live/dead cell staining demonstrated that the ACECM possessed good cell affinity, which favored cell adherence and proliferation. The MSCs that had been labeled with the fluorescent dye PKH26 and seeded on scaffolds were implanted into nude mice. The differentiated cells/ACECM implants formed cartilage-like tissue 4 weeks after implantation, and stained positive for collagen type II and toluidine blue. In addition,the in vivo fluorescent images verified that the MSCs in the implants were the labeled MSCs. These results demonstrated that the oriented ACECM scaffolds hold great promise for use in cartilage tissue engineering applications.

Effects of Green Tea on Blood Pressure and Hypertension-induced Cardiovascular Damage in Spontaneously Hypertensive Rat

Yue-Rong Liang,Shi-Cheng Ma,Xin-Qiang Zheng,Jing-Yi Xu,Ming-Yan Wu,Yi-Wen Luo,Xian-Yang Luo,Jian-Liang Lu 한국식품과학회 2011 Food Science and Biotechnology Vol.20 No.1

Three groups of spontaneously hypertensive rats were administered by gavage with distilled water (control group), low-dose green tea (LGT, 0.2 g/kg BW·day) and high-dose green tea (HGT, 1.0 g/kg BW·day) for 4 weeks,during which systolic blood pressure (SBP) was measured weekly by non-invasive tail-cuff method. At the end of experiment, left ventricular hypertrophy index (LHVI) and plasma biochemical indicators were determined, and ultrastructures of myocardium and aortic vascular smooth muscle cells were observed by transmission electron microscopy (TEM). The results show that green tea gavage suppressed the increase in SBP, along with decline in levels of plasma nitric oxide, aldosterone, malondialdehyde, and LHVI, but increased levels of plasma creatinine, calcitonin gene-related peptide, and glutathione peroxidase in a dose dependant manner. Green tea had no effect on plasma total cholesterol. TEM shows that green tea gavage protected mitochondria of left ventricular myocardium and aortic vascular smooth muscle cells from damage.

Development of a multiplex qRT-PCR assay for detection of African swine fever virus, classical swine fever virus and porcine reproductive and respiratory syndrome virus

Yating Chen,Kaichuang Shi,Huixin Liu,Yanwen Yin,Jing Zhao,Feng Long,Wenjun Lu,Hongbin Si 대한수의학회 2021 Journal of Veterinary Science Vol.22 No.6

Background: African swine fever virus (ASFV), classical swine fever virus (CSFV), and porcine reproductive and respiratory syndrome virus (PRRSV) are still prevalent in many regions of China. Co-infections make it difficult to distinguish their clinical symptoms and pathological changes. Therefore, a rapid and specific method is needed for the differential detection of these pathogens. Objectives: The aim of this study was to develop a multiplex real-time quantitative reverse transcription polymerase chain reaction (multiplex qRT-PCR) for the simultaneous differential detection of ASFV, CSFV, and PRRSV. Methods: Three pairs of primers and TaqMan probes targeting the ASFV p72 gene, CSFV 5′ untranslated region, and PRRSV ORF7 gene were designed. After optimizing the reaction conditions, including the annealing temperature, primer concentration, and probe concentration, multiplex qRT-PCR for simultaneous and differential detection of ASFV, CSFV, and PRRSV was developed. Subsequently, 1,143 clinical samples were detected to verify the practicality of the assay. Results: The multiplex qRT-PCR assay could specifically and simultaneously detect the ASFV, CSFV, and PRRSV with a detection limit of 1.78 × 100 copies for the ASFV, CSFV, and PRRSV, but could not amplify the other major porcine viruses, such as pseudorabies virus, porcine circovirus type 1 (PCV1), PCV2, PCV3, foot-and-mouth disease virus, porcine parvovirus, atypical porcine pestivirus, and Senecavirus A. The assay had good repeatability with coefficients of variation of intra- and inter-assay of less than 1.2%. Finally, the assay was used to detect 1,143 clinical samples to evaluate its practicality in the field. The positive rates of ASFV, CSFV, and PRRSV were 25.63%, 9.36%, and 17.50%, respectively. The co-infection rates of ASFV+CSFV, ASFV+PRRSV, CSFV+PRRSV, and ASFV+CSFV+PRRSV were 2.45%, 2.36%, 1.57%, and 0.17%, respectively. Conclusions: The multiplex qRT-PCR developed in this study could provide a rapid, sensitive, specific diagnostic tool for the simultaneous and differential detection of ASFV, CSFV, and PRRSV.

Define of Optimal Addition Period of Osteogenic Peptide to Accelerate the Osteogenic Differentiation of Human Pluripotent Stem Cells

Song Yameng,Li Hongjiao,Wang Zixuan,Shi Jiamin,Li Jing,Wang Lu,Liao Lingzi,Ma Shengqin,Zhang Yun,Liu Bin,Yang Yaling,Zhou Ping 한국조직공학과 재생의학회 2024 조직공학과 재생의학 Vol.21 No.2

Background: The addition of growth factiors is commonly applied to improve the osteogenic differentiation of stem cells. However, for human pluripotent stem cells (hPSCs), their complex differentiation processes result in the unknown effect at different stages. In this study, we focused on the widely used bone forming peptide-1 (BFP-1) and investigated the effect and mechanisms of its addition on the osteogenic induction of hPSCs as a function of the supplementation period. Methods: Monolayer-cultured hPSCs were cultured in osteogenic induction medium for 28 days, and the effect of BFP-1 peptide addition at varying weeks was examined. After differentiation for varying days (0, 7, 14, 21 and 28), the differentiation efficiency was determined by RT–PCR, flow cytometry, immunofluorescence, and alizarin red staining assays. Moreover, the expression of marker genes related to germ layers and epithelial-mesenchymal transition (EMT) was investigated at day 7. Results: Peptide treatment during the first week promoted the generation of mesoderm cells and mesenchymal-like cells from hiPSCs. Then, the upregulated expression of osteogenesis marker genes/proteins was detected in both hESCs and hiPSCs during subsequent inductions with BFP-1 peptide treatment. Fortunately, further experimental design confirmed that treating the BFP-1 peptide during 7–21 days showed even better performance for hESCs but was ineffective for hiPSCs. Conclusion: The differentiation efficiency of cells could be improved by determining the optimal treatment period. Our study has great value in maximizing the differentiation of hPSCs by adding osteogenesis peptides based on the revealed mechanisms and promoting the application of hPSCs in bone tissue regeneration. Background: The addition of growth factiors is commonly applied to improve the osteogenic differentiation of stem cells. However, for human pluripotent stem cells (hPSCs), their complex differentiation processes result in the unknown effect at different stages. In this study, we focused on the widely used bone forming peptide-1 (BFP-1) and investigated the effect and mechanisms of its addition on the osteogenic induction of hPSCs as a function of the supplementation period. Methods: Monolayer-cultured hPSCs were cultured in osteogenic induction medium for 28 days, and the effect of BFP-1 peptide addition at varying weeks was examined. After differentiation for varying days (0, 7, 14, 21 and 28), the differentiation efficiency was determined by RT–PCR, flow cytometry, immunofluorescence, and alizarin red staining assays. Moreover, the expression of marker genes related to germ layers and epithelial-mesenchymal transition (EMT) was investigated at day 7. Results: Peptide treatment during the first week promoted the generation of mesoderm cells and mesenchymal-like cells from hiPSCs. Then, the upregulated expression of osteogenesis marker genes/proteins was detected in both hESCs and hiPSCs during subsequent inductions with BFP-1 peptide treatment. Fortunately, further experimental design confirmed that treating the BFP-1 peptide during 7–21 days showed even better performance for hESCs but was ineffective for hiPSCs. Conclusion: The differentiation efficiency of cells could be improved by determining the optimal treatment period. Our study has great value in maximizing the differentiation of hPSCs by adding osteogenesis peptides based on the revealed mechanisms and promoting the application of hPSCs in bone tissue regeneration.