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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.
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.
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.
A multifunctional nanoporous layer created on glass through a simple alkali corrosion process
Xiong, Junjie,Das, Sachindra Nath,Kar, Jyoti Prakash,Choi, Ji-Hyuk,Myoung, Jae-Min Royal Society of Chemistry 2010 Journal of materials chemistry Vol.20 No.45
<P>Transparency of the glass substrate plays an important role in the performance of many optical and electronic devices. Herein, the authors have demonstrated a simple method to create a high performance wide–range anti-reflection layer on a glass surface by “carving” it with a hot alkali solution (95 °C). Morphology, composition, surface and optical properties were controlled by changing both the original composition of the glass substrates and etching time. Enhanced transparency (up to 97.7%) was achieved in a wide wavelength range. Superhydrophilic and antifogging properties were also demonstrated, which provide an advantage for optical and opto-electrical devices operating outdoors, in high humidity environments or underwater. In addition, the etched glass surfaces were modified to become hydrophobic (even superhydrophobic) by n-octadecyltrichlorosilane treatment. The glass etching mechanism was investigated and verified using energy dispersive spectra (EDS) and Fourier transform infrared (FTIR) absorption spectra analyses.</P> <P>Graphic Abstract</P><P>Nanoporous layer created on a glass surface by a simple alkali etching process demonstrates high transparency, low reflectance, superhydrophilic and antifogging properties. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c0jm01695k'> </P>
Xiong, Jiu-Qiang,Kurade, Mayur B.,Patil, Dilip V.,Jang, Min,Paeng, Ki-Jung,Jeon, Byong-Hun Elsevier 2017 Algal research Vol.25 No.-
<P><B>Abstract</B></P> <P>Levofloxacin (LEV), a fluoroquinolone antibiotic has been frequently observed in water resources imposing ecotoxicological effects on aquatic microbiota. The biodegradation and metabolic fate of LEV via a microalga, <I>Scenedesmus obliquus</I> in synthetic saline wastewater were investigated in this study. LEV removal (1mgL<SUP>−1</SUP>) by <I>S. obliquus</I> was relatively low in the synthetic wastewater without the addition of sodium chloride (NaCl); however, its removal increased significantly from 4.5 to 93.4% with increasing of its salinity from 0 to 171mM NaCl. Kinetic studies showed that the removal rate constant (k) increased from 0.005 to 0.289d<SUP>−1</SUP> and degradation half-life decreased from 272 to 5d in the presence of NaCl (0–856mM). The removal mechanism analysis showed that the major mechanism of NaCl mediated enhancement of LEV removal was the bioaccumulation and subsequent intracellular biodegradation of LEV in microalgal cells. Six metabolites were identified via gas chromatography–mass spectrometry analysis after biodegradation of LEV. A metabolic pathway was postulated with regard to various cellular biocatalytic reactions in <I>S. obliquus</I>, including decarboxylation, demethylation, dehydroxylation, side chain breakdown, and ring cleavage.</P> <P><B>Highlights</B></P> <P> <UL> <LI> <I>Scenedesmus obliquus</I> was tolerant to levofloxacin, and could withstand its high doses. </LI> <LI> 96h EC<SUB>50</SUB> of levofloxacin for <I>C. vulgaris</I> was 65mgL<SUP>−1</SUP>. </LI> <LI> Addition of NaCl stimulated the biodegradation of levofloxacin up to 93.4%. </LI> <LI> <I>Scenedesmus obliquus</I> can biotransform levofloxacin in simple metabolic byproducts. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Directed Evolution of Beta-galactosidase from Escherichia coli into Beta-glucuronidase
Xiong, Ai-Sheng,Peng, Ri-He,Zhuang, Jing,Liu, Jin-Ge,Xu, Fang,Cai, Bin,Guo, Zhao-Kui,Qiao, Yu-Shan,Chen, Jian-Min,Zhang, Zhen,Yao, Quan-Hong Korean Society for Biochemistry and Molecular Biol 2007 Journal of biochemistry and molecular biology Vol.40 No.3
In vitro directed evolution through DNA shuffling is a powerful molecular tool for creation of new biological phenotypes. E. coli $\beta$-galactosidase and $\beta$-glucuronidase are widely used, and their biological function, catalytic mechanism, and molecular structures are well characterized. We applied an in vitro directed evolution strategy through DNA shuffling and obtained five mutants named YG6764, YG6768, YG6769, YG6770 and YG6771 after two rounds of DNA shuffling and screening, which exhibited more $\beta$-glucuronidase activity than wild-type $\beta$-galactosidase. These variants had mutations at fourteen nucleic acid sites, resulting in changes in ten amino acids: S193N, T266A, Q267R, V411A, D448G, G466A, L527I, M543I, Q626R and Q951R. We expressed and purified those mutant proteins. Compared to the wild-type protein, five mutant proteins exhibited high $\beta$-glucuronidase activity. The comparison of molecular models of the mutated and wildtype enzymes revealed the relationship between protein function and structural modification.
Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota.
Liu, Min-Jiao,Zhu, Wen-Yong,Li, Jie,Zhao, Guo-Zhen,Xiong, Zhi,Park, Dong-Jin,Hozzein, Wael N,Kim, Chang-Jin,Li, Wen-Jun Society for General Microbiology 2015 International journal of systematic and evolutiona Vol.65 No.8
<P>An actinomycete strain, designated YIM 690008T, was isolated from Daucus carota collected from South Korea and its taxonomic position was investigated by using a polyphasic approach. The strain grew well on most media tested and no diffusible pigment was produced. The aerial mycelium formed wrinkled single spores and short spore chains, some of which were branched. The whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, mannose, ribose, galactose and rhamnose. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-10(H2). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, some unknown phospholipids, glycolipids and polar lipids. The major fatty acids were i-C16?:?0, ai-C17?:?0 and C18?:?1ω9c. The DNA G+C content of the genomic DNA was 63.1?mol%. Phylogenetic analysis indicated that the isolate belongs to the family Nocardiopsaceae. However, based on phenotypic, chemotaxonomic and genotypic data, it was concluded that strain YIM 690008T represents a novel genus and novel species of the family Nocardiopsaceae, for which the name Actinorugispora endophytica gen. nov., sp. nov. (type strain YIM 690008T?=?DSM 46770T?=?JCM 30099T?=?KCTC 29480T) is proposed.</P>