Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens)

Bao Qi,Zhang Xiaolan,Bao Pengjia,Liang Chunnian,Guo Xian,Chu Min,Yan Ping 한국유전학회 2021 Genes & Genomics Vol.43 No.10

Background As a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low temperature, scarce food, especially low oxygen) of Qinghai-Tibet Plateau (QTP) after a long process of natural selection. Objective Here, we used Weighted Correlation Network Analysis (WGCNA), a systematic biology method, to identify hypoxic adaptation-related modules and hub genes. The research of the adaptability of yak against hypoxia is of great signifcance to identify the genetic characteristics and yak breeding. Methods Based on the transcriptome sequencing data (PRJNA362606), the R package DESeq2 and WGCNA were conducted to analyze diferentially expressed genes (DEGs) and construct the gene co-expression network. The module hub genes were identifed and characterized by the correlation of gene and trait, module membership (kME). In addition, GO and KEGG enrichment analyses were used to explore the functions of hub genes. Results Our results revealed that 1098, 1429, and 1645 DEGs were identifed in muscle, spleen, and lung, respectively. Besides, a total of 13 gene co-expression modules were detected, of which two hypoxic adaptation-related modules (saddlebrown and turquoise) were found. We identifed 39 and 150 hub genes in these two modules. Functional enrichment analyses showed that 12 GO terms and 18 KEGG pathways were enriched in the saddlebrown module while 85 GO terms and 22 KEGG pathways were enriched in the turquoise module. The signifcant pathways related to hypoxia adaptation include FoxO signaling pathway, Thermogenesis pathway, and Retrograde endocannabinoid signaling pathway, etc. Conclusions In this study, we obtained two hypoxia-related specifc modules and identifed hub genes based on the connectivity by constructing a weighted gene co-expression network. Function enrichment analysis of two modules revealed mitochondrion is the most important organelle for hypoxia adaptation. Moreover, the insulin-related pathways and thermogenic-related pathways played a major role. The results of this study provide theoretical guidance for further understanding the molecular mechanism of yak adaptation to hypoxia.

Effects of inoculating different mycorrhizal fungi on rhizosphere soil fungi and nutrient uptake of blueberry

Song Zejun,Xiao Longhai,Guo Xiaolan,Zhu Yunzheng,An Xiaoli,Tan Yi,Zhang Xinyu,Wang Delu 한국원예학회 2024 Horticulture, Environment, and Biotechnology Vol.65 No.1

The aim of this study was to explore the eff ects of inoculating with diff erent fungi on the structural characteristics of soil fungal communities and the nutrient absorption of blueberry plants. The fungi DSE ( Phialocephala fortinii ), SS ( Penicillium pinophilum ), ZB ( Cladosporium cladosporioides ), QMK ( Chaetomium globosum ), and LZ ( Schizophyllum commune ) were selected for this study. The soil fungal diversity and community structure in the blueberry rhizosphere were compared after inoculation with these diff erent mycorrhizal fungi. The fungal diversity in the blueberry rhizosphere soil was signifi cantly higher after inoculation with DSE, QMK, and ZB than after inoculation with SS and LZ. The dominant class, order, family, and genus of soil fungi were Eurotiomycetes (25.49–36.91%), Eurotiales (24.78–35.00%), Aspergillaceae (24.47–34.74%), and Penicllium (24.34–34.63%), respectively. Among all the fungal treatments, DSE led to the highest abundance of dominant classes, orders, families, and genera. Inoculation with SS, LZ, and DSE increased the contents of nitrogen, phosphorus, and potassium in blueberry plants. The uptake of nitrogen, phosphorus, and potassium were highest in DSE-inoculated plants. The nitrogen content was signifi cantly higher in ZB-inoculated plants than in the control. A TOPSIS analysis showed that among the fi ve fungi, DSE was the best strain to improve the diversity of the blueberry rhizosphere fungal community and promote nutrient uptake by blueberry plants, followed by LZ and ZB. These fi ndings provide scientifi c data for the develop ment and utilization of soil microbial resources, and provide useful information for improving the cultivation and production of blueberries.

Measurement of the Intestinal Digestibility of Rumen Undegraded Protein Using Different Methods and Correlation Analysis

Y. Wang,Y.G. Zhang,Xiaolan Liu,N.K. Kopparapu,Hangshu Xin,J. Liu,Jianhua Guo 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.10

Four methods were adopted, including the mobile nylon bag (MNB) method, modified three-step in vitro (MTS) method, original three-step in vitro (OTS) method, and acid detergent insoluble nitrogen (ADIN) estimating method, to evaluate the intestinal digestibility of rumen undegradable protein (DRUP) of 10 types of concentrates and 7 types of roughages. After correlation analysis to determine the DRUP values using the MNB, MTS, OTS, and ADIN methods, the study aimed to find out appropriate methods to replace the MNB method due to its disadvantages such as high price, long time period, and use of a duodenal T-fistula. Three dairy cows with a permanent ruminal fistula and duodenal T-fistula were used in a single-factor experimental design. The results showed that the determined DRUP values using the MNB method for soybean meal, cottonseed meal, rapeseed meal, sunflower meal, corn germ meal, corn, rice bran, barley, wheat bran, corn fiber feed, Alfalfa (Zhao dong), Alfalfa (Long mu 801), Alfalfa (Long mu 803), grass (North), Grass (Inner Mongolia), corn silage and corn straw were 98.13%, 87.37%, 88.47%, 82.60%, 75.40%, 93.23%, 69.27%, 91.27%, 72.37%, 79.03%, 66.72%, 68.64%, 73.57%, 50.47%, 51.52%, 54.05%, and 43.84%, respectively. The coefficient of determination (R2 = 0.964) of the results between the MTS method and the MNB method was higher than that (R2 = 0.942) between the OTS method and the MNB method. The coefficient of determination of the DRUP values of the concentrates among the in vitro method (including the MTS and OTS methods) and the MNB method was higher than that of the roughage. There was a weak correlation between the determined DRUP values in concentrates obtained from the ADIN method and those from the MNB method, and there was a significant correlation (p<0.01) between the determined DRUP values of the roughage obtained from the MNB method and those obtained from ADIN method. The DRUP values were significantly correlated with the nutritional ingredients of the feeds. The regression equation was DRUP =100.5566+0.4169CP – 0.4344SP – 0.7102NDF – 0.7950EE (R2 = 0.8668, p<0.01; CP, crude protein; SP, soluble protein; NDF, neutral detergent fiber; EE, ether extract). It was concluded that both the MTS method and the OTS may suitable to replace the MNB method for determining the DRUP values and the former method was more effective. Only the ADIN method could be used to predict the values of the roughages but conventional nutritional ingredients were available for all of the samples’ DRUP.

High-accuracy servo press system for the clinching joint process

Chen Liu,Sheng-Dun Zhao,Xiaolan Han,Tong Guo 대한기계학회 2017 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.31 No.2

This paper focuses on the quality improvements on clinching joints using a servo press with a Radial basis function neural network and a sliding mode (RBFS) control strategy. Bottom thickness, which is affected by the press punch position, is usually used to monitor clinching joint quality. Traditional clinching presses are driven by pneumatic pistons or motors that provide feedback on punch force or motor position. However, this feedback is indirectly related to the joint bottom thickness. Clinching workers who set the control parameters on these presses depend on tests and statistics. Thus, this paper presents a servo press system that utilizes punch position feedback to directly control the joint bottom thickness. Transmission errors are considered for the movement accuracy of the servo press. A mathematical model of the servo press is established for analyzing. An algorithm, which combines RBF neural network and sliding mode, is proposed and applied for press position tracking. This algorithm adopts an RBF neural network to approximate the nominal model of the press system. The update law of the algorithm is based on the Lyapunov function used to prove the stability of a closed-loop system. The sliding mode controller compensates for the neural network error and disturbance. Finally, experiments are executed on the servo press with an RBFS controller. To evaluate the performance of the proposed method, a fuzzy PID controller is also applied to the press for comparison. The results indicate that the servo clinching press system with RBFS efficiently and accurately control the clinching jointing process.

Measurement of the Intestinal Digestibility of Rumen Undegraded Protein Using Different Methods and Correlation Analysis

Wang, Y.,Zhang, Y.G.,Liu, Xiaolan,Kopparapu, N.K.,Xin, Hangshu,Liu, J.,Guo, Jianhua Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.10

Four methods were adopted, including the mobile nylon bag (MNB) method, modified three-step in vitro (MTS) method, original three-step in vitro (OTS) method, and acid detergent insoluble nitrogen (ADIN) estimating method, to evaluate the intestinal digestibility of rumen undegradable protein (DRUP) of 10 types of concentrates and 7 types of roughages. After correlation analysis to determine the DRUP values using the MNB, MTS, OTS, and ADIN methods, the study aimed to find out appropriate methods to replace the MNB method due to its disadvantages such as high price, long time period, and use of a duodenal T-fistula. Three dairy cows with a permanent ruminal fistula and duodenal T-fistula were used in a single-factor experimental design. The results showed that the determined DRUP values using the MNB method for soybean meal, cottonseed meal, rapeseed meal, sunflower meal, corn germ meal, corn, rice bran, barley, wheat bran, corn fiber feed, Alfalfa (Zhao dong), Alfalfa (Long mu 801), Alfalfa (Long mu 803), grass (North), Grass (Inner Mongolia), corn silage and corn straw were 98.13%, 87.37%, 88.47%, 82.60%, 75.40%, 93.23%, 69.27%, 91.27%, 72.37%, 79.03%, 66.72%, 68.64%, 73.57%, 50.47%, 51.52%, 54.05%, and 43.84%, respectively. The coefficient of determination ($R^2=0.964$) of the results between the MTS method and the MNB method was higher than that ($R^2=0.942$) between the OTS method and the MNB method. The coefficient of determination of the DRUP values of the concentrates among the in vitro method (including the MTS and OTS methods) and the MNB method was higher than that of the roughage. There was a weak correlation between the determined DRUP values in concentrates obtained from the ADIN method and those from the MNB method, and there was a significant correlation (p<0.01) between the determined DRUP values of the roughage obtained from the MNB method and those obtained from ADIN method. The DRUP values were significantly correlated with the nutritional ingredients of the feeds. The regression equation was DRUP =100.5566+0.4169CP - 0.4344SP - 0.7102NDF - 0.7950EE ($R^2=0.8668$, p<0.01; CP, crude protein; SP, soluble protein; NDF, neutral detergent fiber; EE, ether extract). It was concluded that both the MTS method and the OTS may suitable to replace the MNB method for determining the DRUP values and the former method was more effective. Only the ADIN method could be used to predict the values of the roughages but conventional nutritional ingredients were available for all of the samples' DRUP.

Valeriana jatamansi Jones Inhibits Rotavirus-Induced Diarrhea via Phosphatidylinositol 3-Kinase/Protein Kinase B Signaling Pathway

( Bin Zhang ),( Yan Wang ),( Chunmao Jiang ),( Caihong Wu ),( Guangfu Guo ),( Xiaolan Chen ),( Shulei Qiu ) 한국미생물 · 생명공학회 2021 Journal of microbiology and biotechnology Vol.31 No.8

Rotavirus (RV), as the main cause of diarrhea in children under 5 years, contributes to various childhood diseases. Valeriana jatamansi Jones is a traditional Chinese herb and possesses antiviral effects. In this study we investigated the potential mechanisms of V. jatamansi Jones in RV-induced diarrhea. MTT assay was performed to evaluate cell proliferation and the diarrhea mice model was constructed using SA11 infection. Mice were administered V. jatamansi Jones and ribavirin. Diarrhea score was used to evaluate the treatment effect. The enzyme-linked immunosorbent assay was performed to detect the level of cytokines. Western blot and quantitative reverse transcription-PCR were used to determine protein and mRNA levels, respectively. Hematoxylin-eosin staining was applied to detect the pathological change of the small intestine. TdT-mediated dUTP nick-end labeling was conducted to determine the apoptosis rate. The results showed V. jatamansi Jones promoted MA104 proliferation. V. jatamansi Jones downregulated phosphatidylinositol 3-kinase (PI3K) and protein kinase B (AKT) in protein level, which was consistent with the immunohistochemistry results. Moreover, V. jatamansi Jones combined with ribavirin regulated interleukin-1β (IL-1β), interferon γ, IL-6, tumor necrosis factor α, and IL-10, and suppressed secretory immunoglobulin A secretion to remove viruses and inhibit dehydration. V. jatamansi Jones + ribavirin facilitated the apoptosis of small intestine cells. In conclusion, V. jatamansi Jones may inhibit RV-induced diarrhea through PI3K/AKT signaling pathway, and could therefore be a potential therapy for diarrhea.

Corrigendum to: Valeriana jatamansi Jones Inhibits Rotavirus-Induced Diarrhea via Phosphatidylinositol 3-Kinase/Protein Kinase B Signaling Pathway

( Bin Zhang ),( Yan Wang ),( Chunmao Jiang ),( Caihong Wu ),( Guangfu Guo ),( Xiaolan Chen ),( Shulei Qiu ) 한국미생물생명공학회 2024 Journal of microbiology and biotechnology Vol.34 No.2

Dihydroartemisinin inhibits HepG2.2.15 proliferation by inducing cellular senescence and autophagy

( Jiang Zou ),( Qiang Ma ),( Ru Sun ),( Jiajing Cai ),( Hebin Liao ),( Lei Xu ),( Jingruo Xia ),( Guangcheng Huang ),( Lihua Yao ),( Yan Cai ),( Xiaowu Zhong ),( Xiaolan Guo ) 생화학분자생물학회(구 한국생화학분자생물학회) 2019 BMB Reports Vol.52 No.8

Dihydroartemisinin (DHA) has been reported to possess anti-cancer activity against many cancers. However, the pharmacologic effect of DHA on HBV-positive hepatocellular carcinoma (HCC) remains unknown. Thus, the objective of the present study was to determine whether DHA could inhibit the proliferation of HepG2.2.15 cells and uncover the underlying mechanisms involved in the effect of DHA on HepG2.2.15 cells. We found that DHA effectively inhibited HepG2.2.15 HCC cell proliferation both in vivo and in vitro. DHA also reduced the migration and tumorigenicity capacity of HepG2.2.15 cells. Regarding the underlying mechanisms, results showed that DHA induced cellular senescence by up-regulating expression levels of proteins such as p-ATM, p-ATR, γ-H₂AX, P53, and P21 involved in DNA damage response. DHA also induced autophagy (green LC3 puncta gathered together and LC3II/LC3I ratio increased through AKT-mTOR pathway suppression). Results also revealed that DHA-induced autophagy was not linked to senescence or cell death. TPP1 (telomere shelterin) overexpression could not rescue DHA-induced anticancer activity (cell proliferation). Moreover, DHA down-regulated TPP1 expression. Gene knockdown of TPP1 caused similar phenotypes and mechanisms as DHA induced phenotypes and mechanisms in HepG2.2.15 cells. These results demonstrate that DHA might inhibit HepG2.2.15 cells proliferation through inducing cellular senescence and autophagy. [BMB Reports 2019; 52(8): 520-525]