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Lei Zhang, Zhenxiang Xi, Mingcheng Wang, Xinyi Guo, Tao Ma
Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato ( s.l .) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis , Idesia , two genera of the Salicaceae sensu stricto ( s...
August 2018: Ecology and Evolution
Changwen Zhang, Yunkai Qie, Tong Yang, Li Wang, E Du, Yan Liu, Yong Xu, Baomin Qiao, Zhihong Zhang
Ribosomal stress is known to increase cancer risk, however, the molecular mechanism underlying its various effects on cancer remains unclear. To decipher this puzzle, we investigated the upstream signaling pathway that might be involved in promoting ribosomal stress that leads to tumor progression. Our results suggested that inhibition of kinase PIM1 attenuated PC3 cell growth and motility following the condensed cellular body and decreased protein translation in PIM1-inhibited cells. In addition, PIM1 was found to be a component of the small 40S ribosomal subunit, and could regulate the expression of RPS7...
September 21, 2018: Carcinogenesis
Xiaofang Liao, Yanhong Zhao, Xiangjun Kong, Aziz Khan, Bujin Zhou, Dongmei Liu, Muhammad Haneef Kashif, Peng Chen, Hong Wang, Ruiyang Zhou
Plant mitochondrial (mt) genomes are species specific due to the vast of foreign DNA migration and frequent recombination of repeated sequences. Sequencing of the mt genome of kenaf (Hibiscus cannabinus) is essential for elucidating its evolutionary characteristics. In the present study, single-molecule real-time sequencing technology (SMRT) was used to sequence the complete mt genome of kenaf. Results showed that the complete kenaf mt genome was 569,915 bp long and consisted of 62 genes, including 36 protein-coding, 3 rRNA and 23 tRNA genes...
August 24, 2018: Scientific Reports
Yanxia Sun, Michael J Moore, Jacob B Landis, Nan Lin, Li Chen, Tao Deng, Jianwen Zhang, Aiping Meng, Shoujun Zhang, Komiljon Sh Tojibaev, Hang Sun, Hengchang Wang
The relationships among the genera of the early-diverging eudicot family Berberidaceae have long been controversial. To resolve these relationships and to better understand plastome evolution within the family, we sequenced the complete plastome sequences of ten Berberidaceae genera, combined these with six existing plastomes for the family, and conducted a series of phylogenomic analyses on the resulting data set. Five of the newly sequenced plastomes were found to possess the typical angiosperm plastome complement of 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes...
November 2018: Molecular Phylogenetics and Evolution
Huaying Yan, Wenhao Guo, Ke Li, Mei Tang, Xinyu Zhao, Yi Lei, Chun-Lai Nie, Zhu Yuan
DESI2 is a novel pro-apoptotic gene. We previously reported that DESI2 overexpression induces S phase arrest and apoptosis by activating checkpoint kinases. This work was to test whether the combination of endostatin, an endogenous antiangiogenic inhibitor, with DESI2 could improve the therapy efficacy in vitro and in vivo. The recombinant plasmid co-expressing DESI2 and endostatin was encapsulated with DOTAP/Cholesterol cationic liposome. Mice bearing CT26 colon carcinoma and LL2 lung cancer were treated with the DNA-liposome complex...
October 1, 2018: Experimental Cell Research
Zhenzhong Wang, Xianglong Yu, Xiaoyu Niu, Jing Yang, Yi Tang, Jingdong Hu, Youxiang Diao
The NS1protein, a nonstructural protein of Tembusu virus, plays a key role in the pathogenesis of TMUV. To research host proteins that interact with NS1 protein, the cDNA library of duck embryo fibroblasts (DEF) was successfully constructed. The recombinant plasmid, pGBKT7-NS1, was transformed into the yeast Y2H to be cloned and tested for autoactivation and toxicity. The autoactivation and toxicity test of bait showed that the yeast two hybrid test could be carried out normally. A total of 7 clones from the library were got by Yeast Two-Hybrid System, and 4 proteins, including RPS7, MORC3, GABARAPL1 and MTSS1, may be interacted with DTMUV NS1 after sequencing and blast...
September 2018: Infection, Genetics and Evolution
Wei-Bing Fan, Ying Wu, Jiao Yang, Khurram Shahzad, Zhong-Hu Li
In general, the chloroplast genomes of angiosperms are considered to be highly conserved and affected little by adaptive evolution. In this study, we tested this hypothesis based on sequence differentiation and adaptive variation in the plastid genomes in the order Dipsacales. We sequenced the plastid genomes of one Adoxaceae species and six Caprifoliaceae species, and together with seven previously released Dipsacales chloroplasts, we determined the sequence variations, evolutionary divergence of the plastid genomes, and phylogeny of Dipsacales species...
2018: Frontiers in Plant Science
Mei Jiang, Haimei Chen, Shuaibing He, Liqiang Wang, Amanda Juan Chen, Chang Liu
To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea , C. microphylla , C. kozlowii , and C. Korshinskii . The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C...
May 9, 2018: International Journal of Molecular Sciences
Hong-Bo Li, Chang-Geng Dai, Chang-Rong Zhang, Yong-Fu He, Hai-Yan Ran, Shi-Hong Chen
The oriental armyworm, Mythimna separata, is a major insect pest in China and other Asian countries. Unfortunately, suitable reference genes for quantitative real-time PCR (qRT-PCR) have not been previously identified in M. separata for normalizing target gene expression. In this study, we evaluated the expression stability of eight candidate genes (18S, ACT, EF1-α, GAPDH, RPS7, RPS13, RPL32 and TUB) in M. separata using the comparative ΔCt method, BestKeeper, Normfinder geNorm and ReFinder, a comprehensive software platform...
2018: PloS One
Maria D Logacheva, Anastasiya A Krinitsina, Maxim S Belenikin, Kamil Khafizov, Evgenii A Konorov, Sergey V Kuptsov, Anna S Speranskaya
BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes. RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns...
December 28, 2017: BMC Plant Biology
Babatunde A Ayodele, Michiko Mirams, Charles N Pagel, Eleanor J Mackie
Chondrocyte hypertrophy makes important contributions to bone development and growth. We have investigated a number of novel cartilage genes identified in a recent transcriptomic study to determine whether they are differentially expressed between different zones of equine foetal growth cartilage. Twelve genes ( ATP6V0D2 , BAK1 , DDX5 , GNB1 , PIP4K2A , RAP1B , RPS7 , SRSF3 , SUB1 , TMSB4 , TPI1 and WSB2 ) were found to be more highly expressed in the zone of hypertrophic chondrocytes than in the reserve or proliferative zones, whereas FOXA3 and SERPINA1 were expressed at lower levels in the hypertrophic zone than in the reserve zone...
December 2017: Bone Reports
Sandro Sacchi, Federica Marinaro, Susanna Xella, Tiziana Marsella, Daniela Tagliasacchi, Antonio La Marca
PURPOSE: Anti-Müllerian hormone (AMH) and forkhead box L2 (FOXL2) are two pivotal genes expressed in human granulosa cells (hGCs) where both genes share similar inhibitory functions on activation and follicular growth in order to preserve the ovarian follicle reserve. Furthermore, AMH and FOXL2 contribute to inhibit steroidogenesis, decreasing or preventing the activation of gonadotrophin-dependent aromatase CYP19A1 cytochrome P450 family 19 subfamily A member 1 (CYP19A1). The purpose of this study is to evaluate the role of AMH in regulating the expression of FOXL2...
September 2017: Journal of Assisted Reproduction and Genetics
Xingwang Xie, Xueyan Wang, Dong Jiang, Jianghua Wang, Ran Fei, Xu Cong, Lai Wei, Yu Wang, Hongsong Chen
Ubiquitinlation of proteins is prevalent and important in both normal and pathological cellular processes. Deubiquitinating enzymes (DUBs) can remove the ubiquitin tags on substrate proteins and dynamically regulate the ubiquitination process. The PPPDE family proteins were predicted to be a novel class of deubiquitinating peptidase, but this has not yet been experimentally proved. Here we validated the deubiquitinating activity of PPPDE1 and revealed its isopeptidase activity against ubiquitin conjugated through Lys 48 and Lys 63...
June 24, 2017: Biochemical and Biophysical Research Communications
Gurusamy Raman, Kyoung Su Choi, SeonJoo Park
Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes...
December 2, 2016: Genes
Gurusamy Raman, Kyoung Su Choi, SeonJoo Park
Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes...
December 2, 2016: Genes
Takuya Ichimura, Kenichi Yoshida, Yusuke Okuno, Toshiaki Yujiri, Kozo Nagai, Masanori Nishi, Yuichi Shiraishi, Hiroo Ueno, Tsutomu Toki, Kenichi Chiba, Hiroko Tanaka, Hideki Muramatsu, Toshiro Hara, Hitoshi Kanno, Seiji Kojima, Satoru Miyano, Etsuro Ito, Seishi Ogawa, Shouichi Ohga
Diamond-Blackfan anemia (DBA) is a pure red cell aplasia that arises from defective ribosomal proteins (RPs). Patients with this rare ribosomopathy present with neonatal anemia and occasional dysmorphism. Clinical heterogeneity and clusters of causative RP genes hamper the diagnosis and perinatal management. We report three mother-and-child pairs of anemia who were finally diagnosed by whole-exome sequencing. Each pair showed distinct disease severity and response to anemia treatment. Only one mother had the diagnostic dysmorphism, including short stature, webbed neck, and thenar hypoplasia...
April 2017: International Journal of Hematology
Taniya Mitra, Ivana Bilic, Michael Hess, Dieter Liebhart
Evaluation of reference genes for expression studies in chickens and turkeys is very much limited and unavailable for various infectious models. In this study, eight candidate reference genes HMBS, HPRT1, TBP, VIM, TFRC, RPLP0, RPL13 and RPS7 were evaluated by five different algorithms (GeNorm, NormFinder, BestKeeper©, delta CT, RefFinder) to assess their stability. In order to analyze a broad variation of tissues, spleen, liver, caecum and caecal tonsil of different aged specific pathogen free (SPF) layer chickens and commercial turkeys, uninfected or infected with the extracellular pathogen Histomonas meleagridis, were included...
October 20, 2016: Veterinary Research
A R Del Valle-Echevarria, W Sanseverino, J Garcia-Mas, M J Havey
Pentatricopeptide repeat (PPR) 336 was identified as the candidate gene for Paternal Sorting of Mitochondria ( Psm ), a nuclear locus that affects the predominant mitochondria transmitted to progenies. Cucumber (Cucumis sativus L.) is a useful plant to study organellar-nuclear interactions because its organelles show differential transmission, maternal for chloroplasts and paternal for mitochondria. The mitochondrial DNA (mtDNA) of cucumber is relatively large due in part to accumulation of repetitive DNAs and recombination among these repetitive regions produces structurally polymorphic mtDNAs associated with paternally transmitted mosaic (MSC) phenotypes...
October 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Fay-Wei Li, Li-Yaung Kuo, Kathleen M Pryer, Carl J Rothfels
Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution...
August 25, 2016: Genome Biology and Evolution
Jing Huang, Na Guo, Yinghui Li, Jutao Sun, Guanjun Hu, Haipeng Zhang, Yanfei Li, Xing Zhang, Jinming Zhao, Han Xing, Lijuan Qiu
BACKGROUND: Phytophthora root and stem rot (PRR) caused by Phytophthora sojae is one of the most serious diseases affecting soybean (Glycine max (L.) Merr.) production all over the world. The most economical and environmentally-friendly way to control the disease is the exploration and utilization of resistant varieties. RESULTS: We screened a soybean mini core collection composed of 224 germplasm accessions for resistance against eleven P. sojae isolates. Soybean accessions from the Southern and Huanghuai regions, especially the Hubei, Jiangsu, Sichuan and Fujian provinces, had the most varied and broadest spectrum of resistance...
June 18, 2016: BMC Genetics
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