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Evolutionary dynamics of transposable elements during silkworm domestication
Min‑Jin Han,Hong‑En Xu,Xiao‑Min Xiong,Hua‑Hao Zhang 한국유전학회 2018 Genes & Genomics Vol.40 No.10
Although there are some documented examples on population dynamics of transposable elements (TEs) in model organisms, the evolutionary dynamics of TEs in domesticated species has not been systematically investigated. The objective of this study is to understand population dynamics of TEs during silkworm domestication. In this work, using transposondisplay we examined the polymorphism of seven TE families [they represent about 59% of silkworm (Bombyx mori) total TE content] in four domesticated silkworm populations and one wild silkworm population. Maximum likelihood (ML) was used to estimate selection pressure. Population differentiation and structure were performed by using AMOVA analysis and program DISTRUCT, respectively. The results of transposon-display showed that significant differentiation occurred between the domesticated silkworm and wild silkworm. These TEs have experienced expansions and fixation in the domesticated silkworm but not in wild silkworm. Furthermore, the ML results indicated that purifying selection of TEs in the domesticated silkworm were significantly weaker than that in the wild silkworm. Interestingly, an adaptation insertion induced by BmMITE-2 was found, and this insertion can reduce the polymorphism of the flanking regions of its neighboring COQ7 gene. Our results suggested that TEs expanded and were fixed in the domesticated silkworm might result from demographic effects and artificial selection during domestication. We concluded that the data presented in this study have general implication in animal and crop improvements as well as in domestication of new species.
Identification and evolutionary history of the DD41D transposons in insects
Xiao-Gu Zhang,Hua-Hao Zhang,Yi-Hong Shen,Xiao-Min Xiong,Min-Jin Han 한국유전학회 2016 Genes & Genomics Vol.38 No.2
The rosa monophyletic group of transposons is a group of transposable element with characteristics of encoding a DD41D motif in the catalytic domain. However, biology and evolutionary history of this monophyletic group are still poorly understood. In this study, we report the first description for the presence of a rosa transposon in the silkworm Bombyx mori. Further analyses confirmed that this element in the silkworm genome had recently amplified and might still be capable of transposition. In addition, we present evidence, based on searches of publicly available insect genomes, that a new clade of the rosa monophyletic group was identified. Interestingly, analysis of their three dimensional structures suggested that these proteins showed highly similar protein structures with that of the Mos1 transposase. These results provided useful insights into the functionality of these transposases and their structural and functional deviations from other transposases in the Tc1/mariner superfamily. Meanwhile, sequence and phylogenetic analysis confirmed that DD41D and maT elements might represent another independent large group of the Tc1/mariner superfamily. Importantly, the result of the comparison of terminal inverted repeats (TIRs) validated that DD41D and maT elements almost had identical consensus terminal sequences (50-CAGGGTGNS NCA-30), implying they might have similar cleavage sites or patterns during the process of their transposition. In a word, this study will enrich and expand our knowledge of the Tc1/mariner superfamily.
Xiao-Min Xiong,Shen-Hua Jiang,Guo-Yin Li 한국유전학회 2016 Genes & Genomics Vol.38 No.12
Fourteen novel miniature inverted-repeat transposable element (MITE) families are found in the Florida carpenter ant genome, Camponotus floridanus. They constitute approximately 0.63 % of the entire genome. Analysis of their insertion time showed that most members of these MITEs were inserted into their host genome in less than 8 million years ago. In addition, the association between MITEs and the noncoding regions of genes in C. floridanus is random. Interestingly, an autonomous partner (named CfTEC) responsible for the amplification of these MITEs was also found in C. floridanus. Meanwhile, we present evidence, based on searches of publicly available databases, that this autonomous element was widespread in animals. Moreover, structure and phylogenetic analyses supported that TECs might represent a novel cade of transposons intermediate between the classic CACTA transposon and TRCs. Finally, their transposition mechanism and impact on host genome evolution were also discussed.
( 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]
Zhan-Min Sun,Yan-Min Wu,Mei-Liang Zhou,Xing-Guo Xiao,Yi-Xiong Tang 한국식물생명공학회 2014 Plant biotechnology reports Vol.8 No.4
The APETALA2/ethylene-responsive elementbinding factors (AP2/ERF) play central roles in the stressresponse in plants. In this study, we identified and isolateda novel salt stress-related gene, LcERF080, that encodes anAP2/ERF protein in Lotus corniculatus cultivar Leo. LcERF080 was classified into the B-4 group of the ERFsubfamily based on multiple sequence alignment andphylogenetic characterization. Expression of LcERF080was strongly induced by salt, abscisic acid, 1-aminocyclopropane-1-carboxylic acid, methyl jasmonate, and salicylicacid stresses. Subcellular localization assay confirmedthat LcERF080 is a nuclear protein. LcERF080 overexpressionin Arabidopsis resulted in pleiotropic phenotypeswith a higher seed germination rate and transgenic plantswith enhanced tolerance to salt stress. Further, under stressconditions, the transgenic lines exhibited elevated levels ofsoluble sugars and proline as well as relative moisturecontents but a lower malondialdehyde content than incontrol plants. The expression levels of hyperosmoticsalinity response genes COR15A, RD22, and P5CS1 werefound to be elevated in the LcERF080-overexpressingArabidopsis plants compared to the wild-type plants. Theseresults reveal that LcERF080 is involved in the responsesof plants to salt stress.
Quantized Static Output Feedback Control For Discrete-Time Systems
Chang, Xiao-Heng,Xiong, Jun,Li, Zhi-Min,Park, Ju H. IEEE 2018 IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS - Vol.14 No.8
<P>This paper investigates the problem of output feedback control for discrete-time systems with two quantized signals in measurement output and control input. Since the measurement output and control input are quantized by general quantizers before they are passed to the controller and the system, the closed-loop system will include the quantization error terms, which might lead to that the performance of the closed-loop system is not guaranteed. For this purpose, this paper proposes a novel quantized output control strategy such that the closed-loop system is asymptotically stable or satisfies the prescribed <TEX>$\mathcal {H}_\infty$</TEX> performance. The corresponding design conditions for the output feedback controllers and the quantizers’ dynamic parameters are presented in terms of solutions to a set of linear matrix inequalities. Finally, a simulation example is given to prove the effectiveness of the proposed design method.</P>
Meromorphic Functions Sharing a Nonzero Value with their Derivatives
Li, Xiao-Min,Ullah, Rahman,Piao, Da-Xiong,Yi, Hong-Xun Department of Mathematics 2015 Kyungpook mathematical journal Vol.55 No.1
Let f be a transcendental meromorphic function of finite order in the plane such that $f^{(m)}$ has finitely many zeros for some positive integer $m{\geq}2$. Suppose that $f^{(k)}$ and f share a CM, where $k{\geq}1$ is a positive integer, $a{\neq}0$ is a finite complex value. Then f is an entire function such that $f^{(k)}-a=c(f-a)$, where $c{\neq}0$ is a nonzero constant. The results in this paper are concerning a conjecture of Bruck [5]. An example is provided to show that the results in this paper, in a sense, are the best possible.
Rui Deng,Shi-min Wang,Tao Yin,Ting-hong Ye,Guo-bo Shen, Ling Li,Jing-yi Zhao,Ya-xiong Sang,Xiao-gang Duan,Yu-Quan Wei 한국유방암학회 2014 Journal of breast cancer Vol.17 No.1
Purpose: The universal organic solvent dimethyl sulfoxide (DMSO)can be used as a differentiation inducer of many cancer cells andhas been widely used as a solvent in laboratories. However, itseffects on breast cancer cells are not well understood. The aimof this study is to investigate the effect and associated mechanismsof DMSO on mouse breast cancer. Methods: We appliedDMSO to observe the effect on tumors in a mouse breast cancermodel. Tumor-associated macrophages (TAMs) were tested byflow cytometry. Ex vivo tumor microenvironment was imitated by4T1 cultured cell conditioned medium. Enzyme-linked immunosorbentassays were performed to detect interleukin (IL)-10 andIL-12 expression in medium. To investigate the cytotoxicity ofDMSO on TAMs, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assays were performed. Results: We foundthat DMSO produced tumor retardation when injected into mouseperitoneal cavities in a certain concentration range (0.5–1.0 mg/g). Furthermore, as detected by flow cytometry, TAM subtypeswere found to be transformed. We further imitated a tumor microenvironmentin vitro by using 4T1 cultured cell conditionedmedium. Similarly, by using low concentration DMSO (1.0%–2.0% v/v), TAMs were induced to polarize to the classically activatedmacrophage (M1-type) and inhibited from polarizing intothe alternatively activated macrophage (M2-type) in the conditionedmedium. IL-10 expression in tumors was reduced, whileIL-12 was increased compared with the control. Furthermore, wereported that 2.0% (v/v) DMSO could lead to cytotoxicity in peritonealmacrophages after 48 hours in MTT assays. Conclusion:Our findings suggest that DMSO could exert antitumor effects in4T1 cancer-bearing mice by reversing TAM orientation and polarizationfrom M2- to M1-type TAMs. These data may providenovel insight into studying breast cancer immunotherapy.