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Comparative proteomic analysis of parasitic loranthus seeds exposed to dehydration stress
Limei Pan,Lingyun Wan,Lili He,Lisha Song,Hairong Long,Xiaowen Ji,Ni Jiang,Juan Huo,Shugen Wei,Jine Fu 한국식물생명공학회 2021 Plant biotechnology reports Vol.15 No.1
Parasitic loranthus [Taxillus chinensis (DC.) Danser] is an important medicinal plant that produces recalcitrant seeds that are sensitive to dehydration. Desiccation tolerance is critical for the survival of recalcitrant seeds in low-moisture environments. Clarifying how these seeds respond to desiccation is important for long-term conservation. Thus, the viability, germination, microstructure, and antioxidant enzyme activities of dehydrated parasitic loranthus seeds were investigated. Diverse organelles were degraded or deformed during dehydration treatments. Additionally, superoxide dismutase and catalase activities gradually decreased in response to desiccation stress. A proteomic analysis involving TMT-labeling and LC–MS/ MS were performed. A total of 1479 proteins were identifed, of which 141 were diferentially expressed proteins (DEPs) at 16 and 36 h after initiating the dehydration treatments. A functional annotation based on gene ontology revealed that the DEPs were mainly localized in chloroplasts and were related to energy metabolism, responses to stimuli, and the regulation of biological processes. A KEGG pathway enrichment analysis determined that several of the identifed proteins were associated with signal transductions, photosynthesis, and glycolysis/gluconeogenesis. The results suggest that the efcient removal of excessive ROS amounts may be crucial for promoting parasitic loranthus seed germination under dehydration stress conditions. A series of candidate dehydration stress-related proteins were identifed and may be relevant for enhancing the dehydration tolerance of the recalcitrant seeds. To the best of our knowledge, this is the frst study to elucidate the possible molecular mechanisms underlying the sensitivity of recalcitrant parasitic loranthus seeds to dehydration via a proteomic analysis involving TMT-labeling.
Jiang, Xiao-Cheng,Guo, Xin-Hong,Pan, Xiao-Ling,Song, Song-Quan Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.5
A subtracted cDNA library specific to osmotic stress of Haloxylon ammodendron (Mey.) Bge seedlings was constructed by suppression subtractive hybridization (SSH) and T/A cloning. SSH was performed between two groups of H. ammodendron seedlings, one was cultivated in Hoagland (H) solution as a driver and the other group was treated with osmotic stress of the Hoagland solution by the addition of 400 mM mannitol (M), as a tester. The library consisted of about 400 recombinant clones, with the average size being of 500 bp, ranging from 300 bp to 1500 bp. Using a PCR-select differential screening kit, 100 recombinant clones were randomly chosen from the subtracted cDNA library and hybridized with forward,reverse subtracted and unsubtracted probes for two rounds. As a result, 21 positive clones specific to osmotic stress were obtained and some of them were verified by Northern blot analysis. The sequencing analysis of 6 positive clones and the following homology comparison to GenBank [blastx] non-redundant databases characterized that two sequences obtained in this experiment may contribute to novel drought-related genes.
In silico Discovery of Genes Expressed in Liver, Kidney, Spleen and Small Intestine of Pigs
Pan, Zengxiang,Liu, Honglin,Chen, Jie,Xu, Dan,Jiang, Zhihua,Xie, Zhuang Asian Australasian Association of Animal Productio 2005 Animal Bioscience Vol.18 No.2
An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank "est_others" database using human cDNA sequences as queries to screen the porcine orthologous expressed sequence tags (ESTs), (2) classifying the porcine ESTs records by resources according to certain criteria and (3) analyzing data for ESTs specifically expressed in each organ. In order to do so, four Java programs were developed. Based on the ESTs available in the GenBank database, it was found that there were at least 2,100 genes expressed in these four organs, including 128 in the liver, 81 in the kidney, 780 in the spleen, and 1,423 in the small intestine respectively (a few genes co-expressed in these tissues). Gene expression patterns, such as co-expressed genes, preferentially expressed genes and basic active genes were also compared and characterized among these organs. This study provides a comprehensive model on how to use the bioinformatics approach and Genbank databases to facilitate the discovery of new genes in livestock species.
Pan Li,Zuan-hao Liang,Zhuo Jiang,Ziyou Qiu,Bing Du,Yu-bing Liu,Wen-zhi Li,Li-hao Tan 한국식품과학회 2018 Food Science and Biotechnology Vol.27 No.6
Phthalate plasticizers residue in food is a serious threat to public health. Spores of Ganoderma lucidum are easy to be contaminated with phthalates during collection and processing. In this study, supercritical fluid extraction (SFE) was performed to remove phthalates in spores of G. lucidum, and the effects on acid and peroxide values of spores’ oil were also evaluated. The results showed SFE removed 100% of the residual di-iso-butyl phthalate, di-nbutyl phthalate and di-2-ethylhexyl phthalate in the spores of G. lucidum. No significant differences in polysaccharides content and fatty acid composition were observed between SFE and control spores. However, the triterpenoid extracts of SFE spores had a 7.45% increase, significantly higher than that in control spores. Accelerated oxidation tests further implied that SFE could improve the stability of spores’ oil. Our results suggested SFE is a potential approach to remove phthalate from food related products.
Upregulation and Clinicopathological Significance of Long Non-coding NEAT1 RNA in NSCLC Tissues
Pan, Lin-Jiang,Zhong, Teng-Fei,Tang, Rui-Xue,Li, Ping,Dang, Yi-Wu,Huang, Su-Ning,Chen, Gang Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.7
Background: Recent reports have shown that nuclear enriched abundant transcript 1 (NEAT1), a long noncoding RNA (lncRNA), contributes to the precise control of gene expression and is related to several human malignancies. However, limited data are available on the expression and function of NEAT1 in lung cancer. The major objective of the current study was to profile the expression and clinicopathological significance of NEAT1 in non-small cell lung cancers (NSCLCs). Materials and Methods: NEAT1 expression in 125 NSCLC cases and paired adjacent non-cancer tissues was assessed by real-time quantitative reverse transcription-PCR (qRT-PCR). Relationships between NEAT1 and clinicopathological factors were also investigated. Results: The relative level of NEAT1 was $6.98{\pm}3.74$ in NSCLC tissues, significantly elevated as compared to that of the adjacent non-cancer lung tissues ($4.83{\pm}2.98$, p<0.001). The area under curve (AUC) of high expression of NEAT1 to diagnose NSCLC was 0.684 (95% CI: 0.619~0.750, p<0.001). NEAT1 expression was positively correlated with patient age (r=-2.007, p=0.047), lymphatic metastasis (r=-2.731, p=0.007), vascular invasion (r=-3.617, p=0.001) and clinical TNM stage (r=-4.134, p<0.001). Conclusions: This study indicates that NEAT1 might be associated with oncogenesis and progression in NSCLC, and suggests application in molecular targeted therapy.
Pan, Zengxiang,Zhang, Junlei,Zhang, Jinbi,Zhou, Bo,Chen, Jie,Jiang, Zhihua,Liu, Honglin Asian Australasian Association of Animal Productio 2012 Animal Bioscience Vol.25 No.7
In Erhualian and Yorkshire reciprocal cross $F_1$ pig populations, we examined the mRNA expression characteristic of liver-derived IGF-1, IGF-1R, IGF-2, IGF-2R and IGFBP-3 during the embryonic and postnatal developmental periods (E50, E70, E90, D1, D20, D70, D120 and D180). Our results demonstrated that the IGF-system genes mRNA levels exhibited an ontogenetic expression pattern, which was potentially associated with the porcine embryonic development, postnatal growth, organogenesis and even the initiation and acceleration of puberty. The expression pattern of IGF-system genes showed variation in the reciprocal cross ($F_1$ YE and EY pigs). This study also involved the expression features of imprinted genes IGF-2 and IGF-2R. The parent-of-origin effect of imprinted genes was reflected by their differential expression between the reciprocal crosses populations. The correlation analysis also indicated that the regulatory network and mechanisms involved in the IGF system were a complex issue that needs to be more fully explored. A better understanding of IGF system components and their interactive mechanisms will enable researchers to gain insights not only into animal organogenesis but also into somatic growth development and even reproduction.
Optimal filter based on scale-invariance generation of natural images
Jiang, F.,Chen, B. W.,Rho, S.,Ji, W.,Pan, L.,Guo, H.,Zhao, D. Springer Science + Business Media 2016 The Journal of supercomputing Vol.72 No.1
<P>One of the most striking properties of natural image statistics is the scale invariance. Some earlier studies have assumed that the kurtosis of marginal band pass filter response to be constant throughout scales for a natural image. In our study, this assumption is loosened by adaptively estimating an optimal filter computation whose response distributions through scales have the least Kullback-Leibler divergence. The adaptive filter and its responses characterize the scale-invariance property more accurately and effectively and are further utilized to model the statistics scale-invariance prior in this paper. Extensive experiments on image super-resolution and de-noising manifest that the explored natural images scale-invariance prior model achieves significant performance improvements over the current state-of-the-art schemes.</P>