Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress respo

Xiao‑Xiao Gong,Bing‑Yu Yan,Jin Hu,Cui‑Ping Yang,Yi‑Jian Li,Jin‑Ping Liu,Wen‑Bin Liao 한국유전학회 2018 Genes & Genomics Vol.40 No.11

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (cold treatment at 4 °C for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

Meteorological driven factors of population growth in brown planthopper, Nilaparvata lugens Stål (Hemiptera: Delphacidae), in rice paddies

Xiao‐Zhen Li,Yi ZOU,Hai-Yan YANG,Hai-Jun XIAO,Jian-Guo WANG 한국곤충학회 2017 Entomological Research Vol.47 No.5

Growth of brown planthopper (BPH) (Nilaparvata lugens Stål) in rice paddies is mainly driven by meteorological factors under similar management practices. By analyzing field investigation and meteorological data collected from 2008 to 2013 in Nanchang, China, we show that BPH population densities and monthly growth rates (BGR) changed greatly from May to October, and these changes were closely associated with meteorological factors. Stepwise regression and path analysis indicated average speed of winds (AW) in June and lowest temperature (LT) in July were the first factors entering analysis, which interpreted 46.20% and 31.90% of their influences on BGR. While highest temperature (HT) in August and average temperature (AT) in September were the most important factors affecting BGR, but their direct path coefficients were all smaller than their corresponding indirect path coefficients. In October, relative humidity (RH), AW and number of raining days (RD) had significant effects on BGR. According to the sum of each meteorological factor entering stepwise regression analysis sequences, we found AW had the utmost effect on BPH growth, followed by AT and RH, but LT and RD least. The work demonstrate dynamic meteorological factors driving BPH growth and outbreak in rice paddies, which would facilitate the development of durable approaches for forecasting and controlling this destructive rice pest.

New method for rapidly estimating population densities of the concealed wood‐borer Monochamus alternatus (Coleoptera: Cerambycidae) in the field

Xiao‐Yi Wang,Zhong-qi Yang,Chun-Nan SITU,Jian WANG,Fu-Yong FU 한국곤충학회 2016 Entomological Research Vol.46 No.2

To rapidly estimate pine sawyer, Monochamus alternatus Hope, population densities in forests, the vertical distributions of M. alternatus oviposition sites and larvae on infested Masson pines (Pinus massoniana Lamb.) were studied. Results showed that the number of oviposition sites on sections of trunks between 0 and 2 m above ground was significantly greater than on sections of trunk above 2 m, and the vertical distribution had a significant logarithmic relationship with trunk height. The larval number of M. alternatus on dead infested trees had a significant difference among heights of trunks. Sections on trunks at 2–4 m usually contained the largest number of M. alternatus larvae, while the number of larvae on trunks above 10 m declined significantly, as well as in the 1 m section of trunk at the base. The vertical distribution of M. alternatus larvae on dead infested pines showed a distinct parabolic relationship with trunk height. The number of oviposition sites of M. alternatus on infested Masson pine trunks revealed a significant exponential relationship with the diameter at breast height (DBH) of trees. A significant positive linear relationship also was observed between M. alternatus larval number and DBH on the host pine trees, as well as between the numbers of larvae and oviposition sites on an individual tree. The total number of larvae in an infested tree could be calculated easily using an established equation, through counting the number of oviposition sites at 3–4 m of trunk aboveground. This study developed a practical method for rapid estimation of M. alternatus populations.

Comparison of volatile organic compounds from uninfested and Monochamus alternatus Hope infested Pinus massoniana Lamb.

Xiao‐Juan Li,Guang-Ping DONG,Jian-Min FANG,Hong-Jian LIU,Wan-Lin GUO 한국곤충학회 2017 Entomological Research Vol.47 No.3

Monochamus alternatus is a destructive stem‐boring herbivore of Pinus massoniana, and the principal vector of pine wood nematode. To investigate the impacts of boring by M. alternatus larvae on the emission of volatile organic compounds (VOCs) from their host trees, the VOCs from uninfested and M. alternatus larvae infested P. massoniana trees were observed using a gas chromatograph–mass spectrometer. We detected 12, 9, 18 and 14 volatile organic compounds from infested xylem, infested phloem, uninfested xylem and uninfested phloem, respectively. In P. massoniana xylem, the boring of M. alternatus larvae induced cyclosativene, and inhibited 4‐carene, humulene, styrene, α‐phellandrene, β‐myrcene, β‐phellandrene and γ‐terpinene. The relative amounts of camphene, copacamphene, longicyclene, longifolene, tricyclene and α‐longipinene were significantly increased, and the relative amounts of α‐pinene and β‐pinene were significantly decreased by the boring behaviors of M. alternatus larvae. In P. massoniana phloem, the boring of M. alternatus larvae induced 2‐bornanone, copacamphene, longicyclene and α‐longipinene, and inhibited 2‐carene, 4‐carene, styrene, α‐phellandrene, β‐myrcene, β‐phellandrene, β‐pinene, γ‐terpinene and ο‐cymene. The relative amounts of camphene, caryophyllene and longifolene were significantly increased by the boring behaviors of M. alternatus larvae. The results indicate that the boring behaviors of M. alternatus larvae changed both the sorts and contents of the VOCs from P. massoniana trees.

Identification of differentially expressed immunity‐related genes in Monochamus alternatus Hope (Coleoptera: Cerambycidae) larvae parasitized by Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae)

Xiao‐Juan Li,Guang-Ping DONG,Jian-Min FANG,Hong-Jian LIU,Wan-Lin GUO 한국곤충학회 2018 Entomological Research Vol.48 No.4

The pine sawyer Monochamus alternatus Hope (Coleoptera: Cerambycidae) is a serious pest of several Pinus species, and the ectoparasitoid larvae of Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) is an important natural enemy of this pest. The transcriptome of M. alternatus larvae was sequenced using the Illumina platform and immunity‐related genes were specifically analyzed. De novo assembly resulted in the identification of 24 241 unigenes, with a mean length of 1122 bp, in unparasitized M. alternatus larvae and 23 807 unigenes, with a mean length of 1140 bp, for parasitized larvae. Removal of redundant unigenes resulted in 26 095 all‐unigenes, of which 16 959 (64.99%) showed clear homology with some of the known genes in the National Center for Biotechnology Information nr database. Parasitization had notable effects on the transcriptome profile of M. alternatus larvae. In all, 2702 genes were differentially expressed in M. alternatus larvae after parasitization, with 1491 (55.18%) upregulated and 1211 (44.82%) downregulated. Moreover, expression levels of immunity‐related genes in M. alternatus larvae were markedly altered in response to parasitization by D. helophoroides. In conclusion, the transcriptome profiling data, especially the discovered of immunity‐related genes, help illustrate the molecular mechanisms of parasitism between D. helophoroides and M. alternatus and provide new insights into developing immunity regulation‐mediated control methods of M. alternatus.

The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus

Xiao‑xia Ma,Yi‑ning Wang,Xiao‑an Cao,Xue‑rui Li,Yong‑sheng Liu,Jian‑hua Zhou,Xue‑peng Cai 한국유전학회 2018 Genes & Genomics Vol.40 No.9

The nucleocapsid (N) protein of peste des petits ruminants virus (PPRV) with a conserved amino acid usage pattern plays an important role in viral replication. The primary objective of this study was to estimate roles of synonymous codon usages of PPRV N gene and tRNA abundances of host in the formation of secondary structure of N protein. The potential effects of synonymous codon usages of N gene and tRNA abundances of host on shaping different folding units (α-helix, β-strand and the coil) in N protein were estimated, based on the information about the modeling secondary structure of PPRV N protein. The synonymous codon usage bias was found in different folding units in PPRV N protein. To better understand the role of translation speed caused by variant tRNA abundances in shaping the specific folding unit in N protein, we modeled the changing trends of tRNA abundance at the transition boundaries from one folding unit to another folding unit (β-strand → coil, coil → β-strand, α-helix → coil, coil → α-helix). The obvious fluctuations of tRNA abundance were identified at the two transition boundaries (β-strand → coil and coil → β-strand) in PPRV N protein. Our findings suggested that viral synonymous codon usage bias and cellular tRNA abundance variation might have potential effects on the formation of secondary structure of PPRV N protein.

Postmenopausal Hormone Therapy is Associated with in Situ Breast Cancer Risk

Ni, Xiao-Jian,Xia, Tian-Song,Zhao, Ying-Chun,Ma, Jing-Jing,Zhao, Jie,Liu, Xiao-An,Ding, Qiang,Zha, Xiao-Ming,Wang, Shui Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.8

Background: The relationship between postmenopausal hormone therapy (HT) and invasive breast cancer has been extensively investigated, but that with breast carcinoma in situ (BCIS) has received relatively little attention. The aim of our present study was to review and summarize the evidence provided by longitudinal studies on the association between postmenopausal HT use and BCIS risk. Methods: A comprehensive literature search for articles published up to May 2012 was performed. Prior to performing a meta-analysis, the studies were evaluated for publication bias and heterogeneity. Relative risk (RR) or odds ratio (OR) values were calculated using 14 reports (8 case-control studies and 6 cohort studies), published between 1986 and 2012. Results: There was evidence of an association between ever postmenopausal estrogen use and BCIS based on a random-effects model (RR = 1.25, 95% confidence interval (CI) = 1.01, 1.55). However, we found no strong evidence of an association between ever postmenopausal estrogen combined with progesterone use and BCIS using a randomeffects model (RR = 1.55, 95% CI = 0.95, 2.51). Furthermore, our analysis showed a strong association between "> 5 years duration" of estrogen or estrogen combined with progesterone use and BCIS. Furthermore, current use of any HT is associated with increased risk of BCIS in cohort studies. Additional well-designed large studies are now required to validate this association in different populations.

Relation between Ki-67, ER, PR, Her2/neu, p21, EGFR, and TOP II-α Expression in Invasive Ductal Breast Cancer Patients and Correlations with Prognosis

Yan, Jian,Liu, Xiao-Long,Han, Lu-Zhe,Xiao, Gang,Li, Ning-Lei,Deng, Yi-Nan,Yin, Liang-Chun,Ling, Li-Juan,Yu, Xiao-Yuan,Tan, Can-Liang,Huang, Xiao-Ping,Liu, Li-Xin Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.2

The aim of the present study was to investigate the expression of the transcription factor Ki-67, ER, PR, Her2/neu, p21, EGFR, and TOP II-${\alpha}$ in the tumor tissue of patients with invasive ductal carcinoma(IDC); in addition, we examined correlations between these markers. Two hundred and sixteen IDC patients, who were not previously been treated with chemo- or radiotherapy, were included in the study. All tumors were grade I-III. Expression of molecular markers was determined by immunohistochemical analysis on paraffin-embedded tissue sections. Follow-up data were collected for 3 months to 10 years and analyzed for tumor recurrence, survival time, and prognostic risk factors. We determined Ki-67 expression correlates with the expression of ER, PR, HER-2, EGFR, and TOP-${\alpha}$, as well as lymph node involvement, high tumor grade, lymphovascular invasion, high tumor stage, and high TNM stage in IDC. Positive Ki-67 expression was a risk factor for rapid tumor recurrence and may help tumor progression, leading to poor prognosis in IDC. Ki-67 was directly correlated with EGFR, TOP II-${\alpha}$, lymph node involvement, high tumor grade, lymphovascular invasion, high tumor stage, and high TNM stage in the hormone receptor subtypes of breast cancer. In triple negative breast cancer, Ki-67 correlated with TOP II-${\alpha}$. Expression of Ki-67 correlated with that of ER, PR, HER-2, EGFR, TOP II-${\alpha}$, and p21. In addition, the biomarker Ki-67 has a role as a prognostic factor and indicates a poor prognosis in IDC.

Low Counts of γδ T Cells in Peritumoral Liver Tissue are Related to More Frequent Recurrence in Patients with Hepatocellular Carcinoma after Curative Resection

Cai, Xiao-Yan,Wang, Jia-Xing,Yi, Yong,He, Hong-Wei,Ni, Xiao-Chun,Zhou, Jian,Cheng, Yun-Feng,Jin, Jian-Jun,Fan, Jia,Qiu, Shuang-Jian Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.2

Objectives: TCR-gamma-delta+T cells (${\gamma}{\delta}$ T cells) are non-conventional T lymphocytes that can recognize and eradicate tumor cells. Our previous studies showed that infiltration and function of ${\gamma}{\delta}$ T cells were substantially attenuated in hepatocellular carcinoma (HCC). However, their prognostic value was not clarified. Methods: The association between ${\gamma}{\delta}$ T cells and the clinical outcomes was determined by immunohistochemistry (IHC) in a HCC patient cohort (n = 342). Results:Immunohistochemistry showed decreased infiltration of ${\gamma}{\delta}$ T cells in tumoral tissues compared with paired peritumoral tissues. The counts of ${\gamma}{\delta}$ T cells in peritumoral tissues were negatively correlated with tumor size (P = 0.005). Survival analysis showed that the levels of peritumoral ${\gamma}{\delta}$T cells were related to both time to recurrence (TTR) and overall survival (OS) (P = 0.010 and P = 0.036, respectively) in univariate analysis, and related to TTR in multivariate analysis (P = 0.014, H.R. [95% CI] = 0.682 [0.502-0.927]). Furthermore, the level of peritumoral ${\gamma}{\delta}$ T cells showed independent prognostic value for TTR in Barcelona Clinic Liver Cancer (BCLC) stage A patients (P = 0.038, H.R. [95% CI] = 0.727 [0.537-0.984]). However, tumoral ${\gamma}{\delta}$ T cells did not show independent prognostic value for either TTR or OS in HCC patients. Conclusions: Low counts of ${\gamma}{\delta}$ T cells in peritumoral liver tissue are related to a higher incidence of recurrence in HCC and can predict postoperative recurrence, especially in those with early-stage HCC.

Optimizing the binding activity of the AP2/ERF transcription factor with the GCC box element from Brassica napus by directed evolution

( Xiao Fen Jin ),( Bo Zhu ),( Ri He Peng ),( Hai Hua Jiang ),( Jian Min Chen ),( Jing Zhuang ),( Jian Zhang ),( Quan Hong Yao ),( Ai Sheng Xiong ) 생화학분자생물학회 (구 한국생화학분자생물학회) 2010 BMB Reports Vol.43 No.8

In this study, we cloned the ERF-B3 subfamily transcription factor gene BnaERF-B3-hy15 from Brassica napus L. Huyou15. This 600 bp gene encodes a 199 amino acid classic ethylene responsive factor (ERF), which shown no binding or very weak binding GCC box-binding activity by the yeast one-hybrid assay. We used gene shuffling and the yeast one-hybrid system to obtain three mutated sequences that can bind to the GCC box. Sequence analysis indicated that two residues, Gly156 in the AP2 domain and Phe62 at the N-terminal domain were mutated to arginine and serine, respectively. Changes of Gly156 to arginine and Phe62 to serine increased the GCC- binding activity of BnaERF-B3-hy15 and the alter of Gly156 to arginine changed the AP2-domain structure of BnaERF-B3- hy15. [BMB reports 2010; 43(8): 567-572]