The dynamic transcriptome of waxy maize (Zea mays L. sinensis Kulesh) during seed development

Wei Gu,Diansi Yu,Yuan Guan,Hui Wang,Tao Qin,Pingdong Sun,Yingxiong Hu,Jihui Wei,Hongjian Zheng 한국유전학회 2020 Genes & Genomics Vol.42 No.9

Background Waxy maize (Zea mays L. sinensis Kulesh) is a mutant of maize (Zea mays L.) with a mutation at Waxy1 (Wx1) gene locus. The seed of waxy maize has higher viscosity compared to regular maize. By now, we know little about the expression patterns of genes that involved in the seed development of waxy maize. Objective By analyzing the transcriptome data during waxy maize seed development, we attempt to dig out the genes that may infuence the seed development of waxy maize. Methods The seeds of waxy maize inbred line SWL01 from six phases after pollination were used to do RNA-seq. Bioinformatics methods were used to analyze the expression patterns of the expressed genes, to identify the genes involved in waxy maize seed development. Results A total of 24,546 genes including 1611 transcription factors (TFs) were detected during waxy maize seed development. Coexpression analysis of expressed genes revealed the dynamic processes of waxy maize seed development. Particularly, 2457 genes including 177 TFs were specially expressed in waxy maize seed, some of which mainly involved in the process of seed dormancy and maturation. In addition, 2681, 5686, 4491, 4386, 3669 and 4624 genes were identifed to be diferential expressed genes (DEGs) at six phases compared to regular maize B73, and 113 DEGs among them may be key genes that lead the diference of seed development between waxy and regular maizes in milk stage. Conclusion In summary, we elucidated the expression patterns of expressed genes during waxy maize seed development globally. A series of genes that associated with seed development were identifed in our research, which may provide an important resource for functional study of waxy maize seed development to help molecular assisted breeding.

Helicobacter pylori Proteins Response to Nitric Oxide Stress

Wei Qu,Yabin Zhou,Chunhong Shao,Yundong Sun,Qunye Zhang,Chunyan Chen,Jihui Jia 한국미생물학회 2009 The journal of microbiology Vol.47 No.4

Helicobacter pylori is a highly pathogenic microorganism with various strategies to evade human immune responses. Nitric oxide (NO) and reactive nitrogen species (RNS) generated via nitric oxide synthase pathway are important effectors during the innate immune response. However, the mechanisms of H. pylori to survive the nitrosative stress are not clear. Here the proteomic approach has been used to define the adaptive response of H. pylori to nitrosative stress. Proteomic analysis showed that 38 protein spots were regulated by NO donor, sodium nitroprusside (SNP). These proteins were involved in protein processing, antioxidation, general stress response, and virulence, as well as some unknown functions. Particularly, some of them were participated in iron metabolism, potentially under the control of ferric uptake regulator (Fur). Real time PCR revealed that fur was induced under nitrosative stress, consistent with our deduction. One stress-related protein up-regulated under nitrosative conditions was thioredoxin reductase (TrxR). Inactivation of fur or trxR can lead to increased susceptivity to nitrosative stress respectively. These studies described the adaptive response of H. pylori to nitric oxide stress, and analyzed the relevant role of Fur regulon and TrxR in nitrosative stress management.

Identification of S-Nitrosylation of Proteins of Helicobacter pylori in Response to Nitric Oxide Stress

Wei Qu,Yabin Zhou,Yundong Sun,Ming Fang,Han Yu,Wenjuan Li,Zhifang Liu,Jiping Zeng,Chunyan Chen,Chengjiang Gao,Jihui Jia 한국미생물학회 2011 The journal of microbiology Vol.49 No.2

Innate and adaptive immune responses are activated in humans when Helicobacter pylori invades the gastric mucosa. Nitric oxide (NO) and reactive nitrogen species are important immune effectors, which can exert their functions through oxidation and S-nitrosylation of proteins. S-nitrosoglutathione and sodium nitroprusside were used as NO donors and H. pylori cells were incubated with these compounds to analyze the inhibitory effect of NO. The suppressing effect of NO on H. pylori has been shown in vitro. Furthermore,the proteins modified by S-nitrosylation in H. pylori were identified through the biotin switch method in association with matrix-assisted laser desorption ionization/time-of-flight tandem mass spectrometry (MALDITOF-MS/MS). Five S-nitrosylated proteins identified were a chaperone and heat-shock protein (GroEL),alkyl hydroperoxide reductase (TsaA), urease alpha subunit (UreA), HP0721, and HP0129. Importantly,S-nitrosylation of TsaA and UreA were confirmed using purified recombinant proteins. Considering the importance of these enzymes in antioxidant defenses, adherence, and colonization, NO may exert its antibacterial actions by targeting enzymes through S-nitrosylation. Identification of protein S-nitrosylation may contribute to an understanding of the antibacterial actions of NO. Our findings provide an insight into potential targets for the development of novel therapeutic agents against H. pylori infection.

Effects of gas flow on particulate deposition in EGR coolers

Xun Zhang,Jihui Li,Zhiqiang Han,Xunshun Wu,Wei Tian 대한기계학회 2022 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.36 No.1

This paper presents the test approach to investigate the effects of gas flow rate on particulate deposition inside the exhaust gas recirculation (EGR) coolers. The tests were carried out on a diesel engine equipped with the EGR cooler that a given total gas flow rate passed through and that contained pluggable exchanger tubes to adjust the flow rate in the tubes. Test results show that under the given coolant temperature and EGR gas temperature, the lower flow rate in the exchanger tube is and the longer tubes are, the more particulate with D p > 50 nm deposit in the cooler. With the given total gas flow rate passing through the cooler, the lower flow rate in the exchanger tube is and the longer tubes are, the larger deposit mass is inside the cooler. In the cases of longer tubes, the effects of gas flow rate on the deposit mass are depends on the effects of gas velocity on the particulate deposition, rather than the effects of flow rate on the particulate number passing through the heat exchanger tube per minute.

Oxidation of Zhundong subbituminous coal by Fe2+/H2O2 system under mild conditions

Shuai Chen,Wei Zhou,Mingjun Liu,Guangbo Zhao,Qingxi Cao,Bojun Zhao,Kaikai Kou,Jihui Gao 한국화학공학회 2020 Korean Journal of Chemical Engineering Vol.37 No.4

Oxidation of coal under mild conditions is effective not only to understand the macromolecular network structure of coal but also to produce useful chemicals, allowing more efficient application of coal resources. In this work, the mild oxidation of Zhundong subbituminous coal (ZS) by Fe2+/H2O2 system was carried out under various conditions, including [Fe2+]/[H2O2] molar ratio, temperature, H2O2 concentration and oxidation time. The liquid oxidation products were analyzed using gas chromatography/mass spectrometry (GC/MS), and the chemical structure changes were studied using Fourier transform infrared spectroscopy (FTIR). The results suggest that the oxidation efficiency of ZS with H2O2 is enhanced with the aid of Fe2+. The optimum conditions were determined to be [Fe2+]/[H2O2] molar ratio of 0.00453, H2O2 concentration of 3mol/L, 60 oC and 4 h according to the oxidation conversion rate. In total, 25 compounds were identified, which could be categorized as six group components. Most of them are valuedadded chemicals, and the content of benzene carboxylic acids is the highest among them, making up 29.99% of all group components in total relative content (TRC). -CH2- should be primary bridge connecting the aromatic rings, and alkylene chains linking three aromatic rings are abundant in ZS.

The Changes of Proteomes Components of Helicobacter pylori in Response to Acid Stress without Urea

Chunhong Shao,Qunye Zhang,Wei Tang,Wei Qu,Yabin Zhou,Yundong Sun,Han Yu,Jihui Jia 한국미생물학회 2008 The journal of microbiology Vol.46 No.3

Acid stress is the most obvious challenge Helicobacter pylori encounters in human stomach. The urease system is the basic process used to maintain periplasmic and cytoplasmic pH near neutrality when H. pylori is exposed to acidic condition. However, since the urea concentration in gastric juice is approximately 1 mM, considered possibly insufficient to ensure the survival of H. pylori, it is postulated that additional mechanisms of pH homeostasis may contribute to the acid adaptation in H. pylori. In order to identify the acid-related proteins other than the urease system we have compared the proteome profiles of H. pylori strain 26695 exposed to different levels of external pH (7.4, 6.0, 5.0, 4.0, 3.0, and 2.0) for 30 min in the absence of urea using 2-DE. Differentially expressed proteins were identified by MALDI-TOF-TOF-MS analysis, which turned out to be 36 different proteins. The functions of these proteins included ammonia production, molecular chaperones, energy metabolism, cell envelope, response regulator and some proteins with unknown function. SOM analysis indicated that H. pylori responds to acid stress through multi-mechanisms involving many proteins, which depend on the levels of acidity the cells encounter.