Genome-wide identification and analysis of MIKC-type MADS-box genes expression in Chimonanthus salicifolius

Gui Fang-Fang,Jiang Ge-Ge,Bin Dong,Zhong Shi-Wei,Xiao Zheng,Qiu Fang,Wang Yi-Guang,Yang Li-Yuan,Zhao Hongbo 한국유전학회 2023 Genes & Genomics Vol.45 No.9

Background MIKC type MADS-box transcription factors are one of the largest gene families and play a pivotal role in flowering time and flower development. Chimonanthus salicifolius belongs to the family Calycanthaceae and has a unique flowering time and flowering morphology compared to other Chimonanthus species, but the research on MIKC type MADS-box gene family of C. salicifolius has not been reported. Objective Identification, comprehensive bioinformatic analysis, the expression pattern of MIKC-type MADS-box gene family from different tissues of C. salicifolius. Methods Genome-wide investigation and expression pattern under different tissues of the MIKC-type MADS-box gene family in C. salicifolius, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, promoter cis-acting element were performed. Results A total of 29 MIKC-type MADS-box genes were identified from the whole genome sequencing. Interspecies synteny analysis revealed more significant collinearity between C. salicifolius and the magnoliids species compared to eudicots and monocots. MIKC-type MADS-box genes from the same subfamily share similar distribution patterns, gene structure, and expression patterns. Compared with Arabidopsis thaliana, Nymphaea colorata, and Chimonanthus praecox, the FLC genes were absent in C. salicifolius, while the AGL6 subfamily was expanded in C. salicifolius. The selectively expanded promoter (AGL6) and lack of repressor (FLC) genes may explain the earlier flowering in C. salicifolius. The loss of the AP3 homologous gene in C. salicifolius is probably the primary cause of the morphological distinction between C. salicifolius and C. praecox. The csAGL6a gene is specifically expressed in the flowering process and indicates the potential function of promoting flowering. Conclusion This study offers a genome-wide identification and expression profiling of the MIKC-types MADS-box genes in the C. salicifolius, and establishes the foundation for screening flowering development genes and understanding the potential function of the MIKC-types MADS-box genes in the C. salicifolius.

Microwave-assisted Approach for the Rapid Enzymatic Digestion of Rapeseed Meal

Ju-Fang Li,Fang Wei,Lu-Lu Guo,Gang-You Yuan,Feng-Hong Huang,Mu-Lan Jiang,Yuan-Di Zhao,Xu-Yan Dong,Guang-Ming Li,Hong Chen 한국식품과학회 2010 Food Science and Biotechnology Vol.19 No.2

This study demonstrates the use of a new microwave-assisted approach for accelerating the enzymatic digestion of rapeseed meal. The effects of different microwave parameters, such as the time, temperature, and power level, on the degree of hydrolysis (DH) were investigated by using response surface methodology (RSM). The maximum predicted DH value (10.2%) was in good agreement with the value obtained experimentally using an alkaline protease, which was 12.57% under optimal conditions. In only 7 min, the microwave-assisted method achieved a DH value similar to that obtained by the conventional enzymatic digestion method (4 hr). Therefore,this new technique for rapid enzymatic digestion will improve the application of rapeseed meal in the preparation of protein hydrolysates for use in food and feed.

Development of an automated guidance system for rice transplanter1

( Fang-ming Zhang ),( Xi-ming Feng ),( Yuan Li ),( Beom-soo Shin ),( Ru-jiang Shou ) 한국농업기계학회 2012 한국농업기계학회 학술발표논문집 Vol.17 No.1

An automated guidance system was developed on a rice transplanter. A distributed embedded computer system, one ECC and 5 ECUs, was constructed. Two Kalman filters were formed. The 1^st one, named as global Kalman filter, integrated data of a RTK-GPS, a strapdown attitude sensor, and two encoders. The 2^nd one, named as local Kalman filter, integrated data of a strapdown attitude sensor and two encoders. A PID controller was applied to row following control, whose offset RMS could less than 4 cm at speed of 1.2 m/s. A U-turn controller was also designed that it could control the transplanter in a go-turn-back mode.

Off-Road Machinery Systms Engineering : Development of a Prototype of Guidance System for Rice-transplanter

( Fang Ming Zhang ),( Beom Soo Shin ),( Xi Ming Feng ),( Yuan Li ),( Ri Jiang Shou ) 한국농업기계학회 2013 바이오시스템공학 Vol.38 No.4

Purpose: It is not easy to drive a rice-transplanter avoiding underlapped or overlapped transplanting in paddy fields. An automated guidance system for the riding-type rice-transplanter would be necessary to operate the rice-transplanter autonomously or to assist the beginning drivers as a driving aid. Methods: A prototype of guidance system was composed of embedded computers, RTK-GPS, and a power-steering mechanism. Two Kalman filters were adopted to overcome sparse positioning data (1 Hz) from the RTK-GPS. A global Kalman filter estimated the posture of rice-transplanter every one second, and a local Kalman filter calculated the posture from every new estimation of the global Kalman filter with an interval of 200 ms. A PID controller was applied to the row-following mode control. A control method of U-turning mode was developed as well. A stepping motor with a reduction gear set was used to rotate the shaft of steering wheel. Results:Test trials for U-turning and row-following modes were done in a paddy field after some parameters have been tuned at the ground speed range of 0.3 ~ 1.2 m/s. The minimum RMS error of offset was 3.13 cm at the ground speed of 0.3 m/s while the maximum RMS error was 13.01 cm at 1.2 m/s. The offset RMS error tended to increase as the ground speed increased. The target point distance, LT also affected the system performance and PID controller parameters should be adjusted on different ground speeds. Conclusions: A target angle-based PID controller plus stationary steering angle controller made it possible for the rice-transplanter to steer autonomously by following a reference line accurately and even on U-turning mode. However, as condition in paddy fields is very complicated, the system should control the ground speed that prevents it from deviating too much due to ditch and slope.

Increased Serotonin Signaling Contributes to the Warburg Effect in Pancreatic Tumor Cells Under Metabolic Stress and Promotes Growth of Pancreatic Tumors in Mice

Jiang, Shu-Heng,Li, Jun,Dong, Fang-Yuan,Yang, Jian-Yu,Liu, De-Jun,Yang, Xiao-Mei,Wang, Ya-Hui,Yang, Min-Wei,Fu, Xue-Liang,Zhang, Xiao-Xin,Li, Qing,Pang, Xiu-Feng,Huo, Yan-Miao,Li, Jiao,Zhang, Jun-Feng Elsevier 2017 Gastroenterology Vol.153 No.1

<P><B>Background & Aims</B></P> <P>Desmoplasia and poor vascularity cause severe metabolic stress in pancreatic ductal adenocarcinomas (PDACs). Serotonin (5-HT) is a neuromodulator with neurotransmitter and neuroendocrine functions that contributes to tumorigenesis. We investigated the role of 5-HT signaling in the growth of pancreatic tumors.</P> <P><B>Methods</B></P> <P>We measured the levels of proteins that regulate 5-HT synthesis, packaging, and degradation in pancreata from Kras<SUP>G12D/+</SUP>/Trp53<SUP>R172H/+</SUP>/Pdx1-Cre (KPC) mice, which develop pancreatic tumors, as well as in PDAC cell lines and a tissue microarray containing 81 human PDAC samples. We also analyzed expression levels of proteins involved in 5-HT synthesis and degradation by immunohistochemical analysis of a tissue microarray containing 311 PDAC specimens, and associated expression levels with patient survival times. 5-HT level in 14 matched PDAC tumor and non-tumor tissues were analyzed by ELISA. PDAC cell lines were incubated with 5-HT and cell survival and apoptosis were measured. We analyzed expression of the 5-HT receptor HTR2B in PDAC cells and effects of receptor agonists and antagonists, as well as HTR2B knockdown with small hairpin RNAs. We determined the effects of 5-HT stimulation on gene expression profiles of BxPC-3 cells. Regulation of glycolysis by 5-HT signaling via HTR2B was assessed by immunofluorescence and immunoprecipitation analyses, as well as by determination of the extracellular acid ratio, glucose consumption, and lactate production. Primary PDACs, with or without exposure to SB204741 (a selective antagonist of HTR2B), were grown as xenograft tumors in mice, and SB204741 was administered to tumor-bearing KPC mice; tumor growth and metabolism were measured by imaging analyses.</P> <P><B>Results</B></P> <P>In immunohistochemical analysis of a tissue microarray of PDAC specimens, increased levels of TPH1 and decreased level of MAOA, which regulate 5-HT synthesis and degradation, correlated with stage and size of PDACs and shorter patient survival time. We found levels of 5-HT to be increased in human PDAC tissues compared with non-tumor pancreatic tissues, and PDAC cell lines compared with non-transformed pancreatic cells. Incubation of PDAC cell lines with 5-HT increased proliferation and prevented apoptosis. Agonists of HTR2B, but not other 5-HT receptors, promoted proliferation and prevented apoptosis of PDAC cells. Knockdown of HTR2B in PDAC cells, or incubation of cells with HTR2B inhibitors, reduced their growth as xenograft tumors in mice. We observed a correlation between 5-HT and glycolytic flux in PDAC cells; levels of metabolic enzymes involved in glycolysis, the phosphate pentose pathway, and hexosamine biosynthesis pathway increased significantly in PDAC cells following 5-HT stimulation. 5-HT stimulation led to formation of the HTR2B–LYN–p85 complex, which increased PI3K–Akt–mTOR signaling and the Warburg effect by increasing protein levels of MYC and HIF1A. Administration of SB204741 to KPC mice slowed growth and metabolism of established pancreatic tumors and prolonged survival of the mice.</P> <P><B>Conclusions</B></P> <P>Human PDACs have increased levels of 5-HT, and PDAC cells increase expression of its receptor, HTR2B. These increases allow for tumor glycolysis under metabolic stress and promote growth of pancreatic tumors and PDAC xenograft tumors in mice.</P>

Development of a Prototype of Guidance System for Rice-transplanter

Zhang, Fang-Ming,Shin, Beom-Soo,Feng, Xi-Ming,Li, Yuan,Shou, Ru-Jiang Korean Society for Agricultural Machinery 2013 바이오시스템공학 Vol.38 No.4

Purpose: It is not easy to drive a rice-transplanter avoiding underlapped or overlapped transplanting in paddy fields. An automated guidance system for the riding-type rice-transplanter would be necessary to operate the rice-transplanter autonomously or to assist the beginning drivers as a driving aid. Methods: A prototype of guidance system was composed of embedded computers, RTK-GPS, and a power-steering mechanism. Two Kalman filters were adopted to overcome sparse positioning data (1 Hz) from the RTK-GPS. A global Kalman filter estimated the posture of rice-transplanter every one second, and a local Kalman filter calculated the posture from every new estimation of the global Kalman filter with an interval of 200 ms. A PID controller was applied to the row-following mode control. A control method of U-turning mode was developed as well. A stepping motor with a reduction gear set was used to rotate the shaft of steering wheel. Results: Test trials for U-turning and row-following modes were done in a paddy field after some parameters have been tuned at the ground speed range of 0.3 ~ 1.2 m/s. The minimum RMS error of offset was 3.13 cm at the ground speed of 0.3 m/s while the maximum RMS error was 13.01 cm at 1.2 m/s. The offset RMS error tended to increase as the ground speed increased. The target point distance, LT also affected the system performance and PID controller parameters should be adjusted on different ground speeds. Conclusions: A target angle-based PID controller plus stationary steering angle controller made it possible for the rice-transplanter to steer autonomously by following a reference line accurately and even on U-turning mode. However, as condition in paddy fields is very complicated, the system should control the ground speed that prevents it from deviating too much due to ditch and slope.

Autophagy inhibition through PI3K/Akt increases apoptosis by sodium selenite in NB4 cells

( Yun Ren ),( Fang Huang ),( Yuan Liu ),( Yang Yang ),( Qian Jiang ),( Cai Min Xu ) 생화학분자생물학회 2009 BMB Reports Vol.42 No.9

Molecular Cloning and Expression of cDNA Encoding the Cysteine Proteinase Inhibitor from Upland Cotton

Ming-feng Jiang,Sheng-wei Li,Min Chen,Ying-fan Cai,Yong-fang Xie,Biao Li,Quan Sun,Huai-zhong Jiang,Zheng Pan,Yun-ling Gao,You-Lu Yuan,Yu-zheng Shi 한국식물학회 2009 Journal of Plant Biology Vol.52 No.5

A cDNA encoding a novel cysteine proteinase inhibitor (CPI) was isolated from a gland mutant Xiangmian-18 of upland cotton during the pigments gland forming stage. The cDNA comprises 378 bp and encodes 125 amino acid residues with molecular mass of 13.8 kDa. It contains the conserved motif of cysteine protease inhibitors and belongs to the cystatin superfamily (Gln- Val-Val-Ala-Gly). The deduced amino acid sequences of the domains are highly similar to the normal upland cotton (96.8%). SDS-PAGE and western hybridization analysis showed that the expressed recombinant protein was recombinant CPI. The inhibitory activity of recombinant CPI was 46 u/μg which was measured by inhibiting the protease activity of papain. RT-PCR results indicated that the expression level of developing gland stage was higher than that of undeveloped gland stage.

DNMT3a rs1550117 Polymorphism Association with Increased Risk of Helicobacter pylori Infection

Cao, Xue-Yuan,Jia, Zhi-Fang,Cao, Dong-Hui,Kong, Fei,Jin, Mei-Shan,Suo, Jian,Jiang, Jing Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.10

Background: DNA methyltransferase-3a (DNMT3a) plays significant roles in embryogenesis and the generation of aberrant methylation in carcinogenesis. This study aimed to investigate associations between single nucleotide polymorphisms (SNPs) of the DNMT3a gene and risk of Helicobacter pylori infection, gastric atrophy and gastric cancer. Methods: The subjects comprised 447 patients with gastric cancer; 111 individuals with gastric atrophy and 961 healthy controls. Two SNPs (rs1550117 and rs13420827) of the DNMT3a gene were genotyped by Taqman assay. DNMT3a expression was analyzed in cancer tissues from 89 patients by tissue microarray technique. Odds ratio (ORs) and 95% confidence intervals were calculated by multivariate logistic regression. Results: Among healthy controls, risk of H.pylori infection was significantly higher in subjects with the rs1550117 AA genotype, compared to those with GG/AG genotypes of DNMT3a [OR=2.08, (95%CI: 1.02-4.32)]. However, no significant correlation was found between the two SNPs and risk of developing gastric atrophy or gastric cancer. In addition, no increase in DNMT3a expression was observed in the gastric cancer with H.pylori infection. Conclusions: This study revealed that DNMT3a rs1550117 polymorphism is significantly associated with an increased risk of H. pylori infection, but did not support any evidence for contributions of DNMT3a rs1550117 and rs13420827 to either gastric atrophy or gastric cancer. The biological roles of DNMT3a polymorphisms require further investigation.

rs12904 Polymorphism in the 3'UTR of EFNA1 is Associated with Colorectal Cancer Susceptibility in a Chinese Population

Mao, Ying-Ying,Jing, Fang-Yuan,Jin, Ming-Juan,Li, Ying-Jun,Ding, Ye,Guo, Jing,Wang, Fen-Juan,Jiang, Long-Fang,Chen, Kun Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.9

Accumulated evidence has indicated that Ephrin A1 (EFNA1) is associated with angiogenesis and tumorigenesis in various types of malignancies, including colorectal cancer (CRC). In the current study, we performed an online search using the public microarray database to investigate whether EFNA1 expression might be altered in CRC tissues. We then conducted a case-control study including 306 subjects (102 cases and 204 well-matched controls) in Xiaoshan County to assess any association between genetic polymorphisms in EFNA1 and CRC susceptibility. Searches in the Oncomine expression profiling database revealed EFNA1 to be overexpressed in CRC tissue compared with adjacent normal tissue. The rs12904 G-A variant located in the 3' untranslated region (UTR) of EFNA1 was observed to be associated with CRC susceptibility. Compared with the AA homozygous genotype, those carrying GA genotype had a decreased risk of developing CRC (odds ratio (OR)=0.469, 95% confidence interval (CI): 0.225-0.977, and P=0.043). The association was stronger among smokers and tea drinkers, however, no statistical evidence of interaction between rs12904 polymorphism and smoking or tea drinking on CRC risk was found. Our results suggest that EFNA1 is involved in colorectal tumorigenesis, and rs12904 A>G polymorphism in the 3' UTR of EFNA1 is associated with CRC susceptibility. Larger studies and further mechanistic investigations are warranted to confirm our findings.