Comparison of stomach microRNA transcriptomes of Tibetan and Yorkshire pigs by deep sequencing

Wen‑kui Sun,Yanyue Li,Chi Cheng,Yi‑hui Chen,Kai Zeng,Xiaohui Chen,Yiren Gu,Rui Liu,Xuebin Lv,Rong Gao 한국유전학회 2018 Genes & Genomics Vol.40 No.9

MiRNAs regulate the expression of target genes in diverse cellular processes and hence play important roles in different physiological processes, yet little is known about the stomach microRNAome (miRNAome) of the Tibetan pig. The objective of this experiment was to investigate differentially expressed stomach miRNAs participating in digestion. Firstly, we isolated total RNA by Trizol reagent from three Tibetan and three Yorkshire purebred pigs stomach samples at 90-day-old. Secondly, a comprehensive analysis of Tibetan and Yorkshire pig stomach miRNAomes was performed by small RNA sequencing in the Illumina HiSeq 2000 system. Finally, SYBR Green Real-time RT-PCR was performed to validate the differentially expressed miRNAs. We identified 318 unique miRNAs, 260 were co-expressed in both libraries, 17 and 31 miRNAs were specifically expressed in Tibetan and Yorkshire pigs respectively. Fifty six differentially expressed miRNAs were identified by the identifying differentially expressed genes 6 (IDEG6). Kyoto encyclopedia of genes and genomes analysis revealed that some of the differentially expressed miRNAs were associated with protein and fat digestion. Two differentially expressed miRNAs (miR-214-3p and ssc-un39) participating in the digestion of lipid were identified. Additionally, qRT-PCR results suggested that a higher expression of miR-214-3p in the Tibetan pig stomach could lead to relatively lower expression of calcium-dependent phospholipase A2, which is an enzyme important for the digestion of glycerol phospholipid. This study has delineated the different stomach miRNAs expression patterns of Tibetan and Yorkshire pigs, which would help explain the regulatory mechanisms of miRNAs in digestion of Tibetan pigs, and contribute to utilize a the unique digestion merits of Tibetan pig in future porcine hybridization breeding.

Mitochondrial citrate accumulation drives alveolar epithelial cell necroptosis in lipopolysaccharide-induced acute lung injury

Yang Hui-Hui,Jiang Hui-Ling,Tao Jia-Hao,Zhang Chen-Yu,Xiong Jian-Bing,Yang Jin-Tong,Liu Yu-Biao,Zhong Wen-Jing,Guan Xin-Xin,Duan Jia-Xi,Zhang Yan-Feng,Liu Shao-Kun,Jiang Jian-Xin,Zhou Yong,Guan Cha-Xi 생화학분자생물학회 2022 Experimental and molecular medicine Vol.54 No.-

Necroptosis is the major cause of death in alveolar epithelial cells (AECs) during acute lung injury (ALI). Here, we report a previously unrecognized mechanism for necroptosis. We found an accumulation of mitochondrial citrate (citratemt) in lipopolysaccharide (LPS)-treated AECs because of the downregulation of Idh3α and citrate carrier (CIC, also known as Slc25a1). shRNA- or inhibitor–mediated inhibition of Idh3α and Slc25a1 induced citratemt accumulation and necroptosis in vitro. Mice with AEC-specific Idh3α and Slc25a1 deficiency exhibited exacerbated lung injury and AEC necroptosis. Interestingly, the overexpression of Idh3α and Slc25a1 decreased citratemt levels and rescued AECs from necroptosis. Mechanistically, citratemt accumulation induced mitochondrial fission and excessive mitophagy in AECs. Furthermore, citratemt directly interacted with FUN14 domain-containing protein 1 (FUNDC1) and promoted the interaction of FUNDC1 with dynamin-related protein 1 (DRP1), leading to excessive mitophagy-mediated necroptosis and thereby initiating and promoting ALI. Importantly, necroptosis induced by citratemt accumulation was inhibited in FUNDC1-knockout AECs. We show that citratemt accumulation is a novel target for protection against ALI involving necroptosis.

Association of Polymorphisms in Stress-Related TNFα and NPY Genes with the Metabolic Syndrome in Han and Hui Ethnic Groups

Bu, De-Yun,Ji, Wen-Wu,Bai, Dan,Zhou, Jian,Li, Hai-Xia,Yang, Hui-Fang Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14

Background: Metabolic syndrome (MS) is a cluster of complicated disorders caused by the interactive influencing factors of heredity and environment, which predisposes to many cnacers. Results from epidemic research indicate that stress is tightly related to the pathogenesis of MS and neoplasia. This paper aims to investigate the association between psychological stress and MS with respect to the tumor necrosis factor alpha (TNF${\alpha}$) and neuropeptide Y (NPY) genes in the Han and Hui ethnic groups. Methods: All subjects for this case-control study matched strict enrollment criteria (nationality, gender and age) and lived in the city of Wu Zhong of Ningxia Province in China. The enrolled group contained 102 matched pairs of Hui ethnic individuals and 98 matched pairs of Han ethnic individuals. Enrolled subjects completed the general Symptom Checklist-90 (SCL-90). The TNF${\alpha}$-308G/A variant and NPYrs16147 polymorphism were detected in case (81 males, 119 females) and control (81 males, 119 females) groups by polymerase chain reaction (PCR) amplification. Results: Nine factors of the SCL-90 were found to be statistically different (p<0.05) between case and control groups. The homozygous mutant genotype (AA) and the mutant allele (A) of the TNF${\alpha}$-308G/A gene were less frequently observed in the control population compared to the case group. The odds ratio (95% confidence interval) in "Allele" for MS was 2.28 (1.47-3.53), p=0.0001, while "OR" was 1.11 (0.83-1.47), p=0.15, for the NPYrs16147 gene polymorphism. Conclusions: Psychological stress has been positively associated with MS. A previous study from our group suggested there were differences in the level of psychological stress between Hui and Han ethnic groups. Furthermore, we found that the stress-related TNF${\alpha}$ gene was associated with MS for both Han and Hui ethnic groups. In contrast, NPY may be a possible contributor to MS and associated cancer for the Han ethnic group.

Optimal SVM learning method based on adaptive sparse sampling and granularity shift factor

Hui Wen,Dongshun Jia,Zhiqiang Liu,Hang Xu,Guangtao Hao 한국인터넷정보학회 2022 KSII Transactions on Internet and Information Syst Vol.16 No.4

To improve the training efficiency and generalization performance of a support vector machine (SVM) in a large-scale set, an optimal SVM learning method based on adaptive sparse sampling and the granularity shift factor is presented. The proposed method combines sampling optimization with learner optimization. First, an adaptive sparse sampling method based on the potential function density clustering is designed to adaptively obtain sparse sampling samples, which can achieve a reduction in the training sample set and effectively approximate the spatial structure distribution of the original sample set. A granularity shift factor method is then constructed to optimize the SVM decision hyperplane, which fully considers the neighborhood information of each granularity region in the sparse sampling set. Experiments on an artificial dataset and three benchmark datasets show that the proposed method can achieve a relatively higher training efficiency, as well as ensure a good generalization performance of the learner. Finally, the effectiveness of the proposed method is verified.

Preparation and Thermal Performance of Fullerene-Based Lead Salt

Hui-Juan Guan,Rufang Peng,Bo Jin,Hua Liang,Fengqi Zhao,Xing-Bing Bu,Wen-Jing Han,Shijin Chu 대한화학회 2014 Bulletin of the Korean Chemical Society Vol.35 No.8

C60 is widely investigated because of its unique structure. But its applications in solid propellant seem to be relatively neglected. C60 has more outstanding features than carbon black which is widely used as a catalyst ingredient of solid propellant. To combine the advantages of fullerene and lead salts, another good composite in propellant catalysts, we synthesized a kind of fullerene phenylalanine lead salt (FPL) and explored its thermal performances by differential thermal analysis (DTA) and thermogravimetry analysis (TGA). The results show it undergoes four exothermic processes started from 408 K. Combined TGA and X-ray diffractometer (XRD), the decomposition mechanism of FPL was derived by TG-IR and comparing IR spectra of FPL and its residues after burned to 327 °C, 376 °C and 424 °C, respectively. Effect of FPL on the decomposition characteristic of hexogen (RDX), a type of explosive in propellant, has been investigated using DTA at different heating rate, which shows the decomposition temperatures of the explosive are all reduced by more than 20 K. The corresponding activation energy (Ea) is decreased by 30 kJ·mol−1. So FPL has potential application as a combustion catalyst in solid propellant.

Two New Flavonoids from Dragon’s Blood of Dracaena cambodiana

Wen-Li Mei,Ying Luo,Hai-Yan Shen,Yan-Bo Zeng,Hao Fu Dai,Hui Wang 대한화학회 2013 Bulletin of the Korean Chemical Society Vol.34 No.6

Phytochemical investigation on dragon’s blood of Dracaena cambodiana led to the discovery of two new flavonoid derivatives, cambodianin G (1) and cambodianin H (2). Their structures were elucidated on the basis of detailed spectroscopic analysis, including 1D and 2D NMR techniques and chemical methods. The two compounds were observed to exhibit antibacterial activities against Staphylococcus aureus, and compound 1 showed cytotoxicities against K562 and SGC-7901 cell lines.

Correlation between rearing temperature and the dual cellulolytic system of Coptotermes formosanus Shiraki and its intestinal microenvironment

Wen-Hui Zeng,Zhi-Qiang Li,Bing-Rong Liu,Qiu-Jian Li,Jun-Hong Zhong 한국응용곤충학회 2016 Journal of Asia-Pacific Entomology Vol.19 No.1

The lower termite, Coptotermes formosanus Shiraki, is an important model species for studying the dual cellulolytic system of termites. The effect of rearing temperature on the interaction between the intestinal symbiont community and the host in lignocelluloses digestion was investigated by assaying the activity and gene expression of cellulase, and monitoring the population size of intestinal protozoan community, which was followed by rearing C. formosanus at a temperature gradient (15–37 °C) for 3 d. The results showed that the rearing temperature of C. formosanus had a much greater impact on cellulase activity and gene transcription of the intestinal symbiont than on the host. The transcriptional variations of endogenous and symbiotic cellulase genes presented mutual complement and restrained when C. formosanus living in high temperature environment (32 and 37 °C). Additionally, the optimum survival temperature of Pseudotrichonympha grassii Koidzumi (22 °C) was found lower than that of Holomastigotoides mirabile Koidzumi (28 °C) and Spirotrichonympha leidyi Koidzumi (28 °C).The optimum rearing temperature for cellulase activity and protozoan survival of C. formosanus was found much lower than its optimum temperature for feeding. These findings provide a novel glimpse into host-symbiotic mutualism in lower termite digestion.

A quantitative analysis of the wing outlines of owlflies (Insecta: Neuroptera: Ascalaphidae)

Hui Wen,Heping Yang,Xinli Wang 한국통합생물학회 2015 Animal cells and systems Vol.19 No.2

We quantitatively described and analyzed variation in the wing outlines of owlflies using 135 forewings and 135 hindwings from eight species in five genera. We captured and digitized images of the wing outlines from 135 individual specimens and subjected them to Elliptic Fourier analysis to produce matrices of Fourier coefficients based on 20 harmonics. The first five principal components extracted from the Fourier coefficient matrices described the wing outlines, explaining 94.87% of the total forewing variation and 95.06% of the total hindwing variation. Relationships among species were estimated using multivariate analysis of variance, principal component analysis, and cluster analysis. The results indicated highly significant differences in the wing outlines among the eight owlfly species. Pair-wise comparisons indicated significant differences between 96% of the species pairs based on the forewing outlines and between 100% of the species pairs based on the hindwing outlines. The results of the cluster analysis were partially consistent with the existing classification system of Ascalaphidae. Our results show that quantitative data of wing outlines can effectively differentiate Libelloides from the other four owlfly genera.

Inverse Diamond Search Algorithm for 3D Medical Image Sets Compression

Wen-Jan Chen,Hui-Min Chen 대한전자공학회 2008 ITC-CSCC :International Technical Conference on Ci Vol.2008 No.7

The scheme of motion estimation is introduced to exploit the redundancy between continuous frames of 3D medical image sets in this paper. The proposed scheme is based on inter-frame motion estimation of inverse diamond search algorithm. The residual images are encoded by the Huffman encoder. The test images include five sets of the heart and two sets of the brain MRI images. The average compression ratio of the inverse diamond search algorithm is similar to the JPEG_LS and diamond search algorithm. The inverse diamond search leads to speed improvement around 5 % over diamond search for all the tested MRI sets.

Differential Impacts on Bacterial Composition and Abundance in Rhizosphere Compartments between Al-Tolerant and Al-Sensitive Soybean Genotypes in Acidic Soil

Wen Zhong-Ling,Yang Min-Kai,Fazal Aliya,Liao Yong-Hui,Cheng Lin-Run,Hua Xiao-Mei,Hu Dong-Qing,Shi Ji-Sen,Yang Rong-Wu,Lu Gui-Hua,Qi Jin-Liang,Zhi Hong,Qian Qiu-Ping,Yang Yong-Hua 한국미생물·생명공학회 2020 Journal of microbiology and biotechnology Vol.30 No.8

In this study, two soybean genotypes, i.e., aluminum-tolerant Baxi 10 (BX10) and aluminumsensitive Bendi 2 (BD2), were used as plant materials and acidic red soil was used as growth medium. The soil layers from the inside to the outside of the root are: rhizospheric soil after washing (WRH), rhizospheric soil after brushing (BRH) and rhizospheric soil at two sides (SRH), respectively. The rhizosphere bacterial communities were analyzed by high-throughput sequencing of V4 hypervariable regions of 16S rRNA gene amplicons via Illumina MiSeq. The results of alpha diversity analysis showed that the BRH and SRH of BX10 were significantly lower in community richness than that of BD2, while the WRH exhibited no significant difference between BX10 and BD2. Among the three sampling compartments of the same soybean genotype, WRH had the lowest community richness and diversity while showing the highest coverage. Beta diversity analysis results displayed no significant difference for any compartment between the two genotypes, or among the three different sampling compartments for any same soybean genotype. However, the relative abundance of major bacterial taxa, specifically nitrogen-fixing and/or aluminum-tolerant bacteria, was significantly different in the compartments of the BRH and/or SRH at phylum and genus levels, indicating genotype-dependent variations in rhizosphere bacterial communities. Strikingly, as compared with BRH and SRH, the WRH within the same genotype (BX10 or BD2) always had an enrichment effect on rhizosphere bacteria associated with nitrogen fixation