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Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
Yushuai Wang, Weiqi Liang, Tian Tang
The evolutionary dynamics of the conflict between transposable elements (TEs) and their host genome remain elusive. This conflict will be intense in stress-adapted plants as stress can often reactivate TEs. Mangroves reduce TE load convergently in their adaptation to intertidal environments and thus provide a unique opportunity to address the host-TE conflict and its interaction with stress adaptation. Using the mangrove Rhizophora apiculata as a model, we investigated methylation and short interfering RNA (siRNA) targeting patterns in relation to the abundance and age of long terminal repeat (LTR) retrotransposons...
May 15, 2018: New Phytologist
Antonio Serrato-Capuchina, Daniel R Matute
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition...
May 15, 2018: Genes
Georgi Bonchev, Yvonne Willi
Transposable elements (TE) can constitute a large fraction of plant genomes, yet our understanding of their evolution and fitness effect is still limited. Here we tested several models of evolution that make specific predictions about differences in TE abundance between selfing and outcrossing taxa, and between small and large populations. We estimated TE abundance in multiple populations of North American Arabidopsis lyrata differing in mating system and long-term size, using transposon insertion display on several TE families...
May 14, 2018: New Phytologist
Gaofeng Liu, Yudong Xia, Tongkun Liu, Shaojun Dai, Xilin Hou
Cytosine DNA methylation is a critical epigenetic mechanism in the silencing of transposable elements, imprinting and regulating gene expression. However, little is known about the potential role of mC in response to heat stress. To determine and explore the functions of the dynamic DNA methylome during heat stress, we characterized single-base resolution methylome maps of Brassica rapa and assessed the dynamic changes of mC under heat stress using whole genome bisulfite sequencing. On average, the DNA methylation levels of CG, CHG and CHH are 39...
May 9, 2018: International Journal of Molecular Sciences
Ting-Heng Chou, Jakob R Allen, Dongwoo Hahn, Brian K Leary, Edward F Coyle
The decline in stroke volume (SV) during exercise in the heat has been attributed to either an increase in cutaneous blood flow (CBF) that reduces venous return or an increase in heart rate (HR) that reduces cardiac filling time. However, the evidence supporting each mechanism arises under experimental conditions with different skin temperatures (Tsk ) (e.g.; {greater than or equal to}38{degree sign}C vs. {less than or equal to}36{degree sign}C respectively). We systematically studied cardiovascular responses to progressively increased Tsk (32{degree sign}C to 39{degree sign}C) with narrowing of the core-to-skin gradient during moderate intensity exercise...
May 10, 2018: Journal of Applied Physiology
Sophia Wunder, Alexander Hunold, Patrique Fiedler, Falk Schlegelmilch, Klaus Schellhorn, Jens Haueisen
Neuromodulation induced by transcranial electric stimulation (TES) exhibited promising potential for clinical practice. However, the underlying mechanisms remain subject of research. The combination of TES and electroencephalography (EEG) offers great potential for investigating these mechanisms and brain function in general, especially when performed simultaneously. In conventional applications, the combination of EEG and TES suffers from limitations on the electrode level (gel for electrode-skin interface) and the usability level (preparation time, reproducibility of positioning)...
May 8, 2018: Scientific Reports
J Auvinet, P Graça, L Belkadi, L Petit, E Bonnivard, A Dettaï, W H Detrich, C Ozouf-Costaz, D Higuet
BACKGROUND: The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus Trematomus (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity...
May 9, 2018: BMC Genomics
Daniel Elsner, Karen Meusemann, Judith Korb
Social insects are promising new models in aging research. Within single colonies, longevity differences of several magnitudes exist that can be found elsewhere only between different species. Reproducing queens (and, in termites, also kings) can live for several decades, whereas sterile workers often have a lifespan of a few weeks only. We studied aging in the wild in a highly social insect, the termite Macrotermes bellicosus , which has one of the most pronounced longevity differences between reproductives and workers...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
Xuan Zhu, Jingzi Beiyuan, Abbe Y T Lau, Season S Chen, Daniel C W Tsang, Nigel J D Graham, Daohui Lin, Jianteng Sun, Yanheng Pan, Xin Yang, Xiang-Dong Li
Polybrominated diphenyl ethers (PBDEs) are common pollutants released from electronic waste (e-waste) dismantling and recycling activities. Our city-wide survey of agricultural soils in Qingyuan (40 sampling sites), where e-waste recycling has been active, observed exceedance of PBDEs above background levels (average of 251.9ngg-1 , 87 times the regional baseline concentration) together with elevated levels of metals/metalloids at the contamination hotspots, such as As (180.4mgkg-1 ), Cu (100.7mgkg-1 ), Zn (93...
April 1, 2018: Science of the Total Environment
Svenja Mager, Uwe Ludewig
DNA methylation in plants plays a role in transposon silencing, genome stability and gene expression regulation. Environmental factors alter the methylation pattern of DNA and recently nutrient stresses, such as phosphate starvation, were shown to alter DNA methylation. Furthermore, DNA methylation had been frequently addressed in plants with notably small genomes that are poor in transposons. Here, we compare part of the DNA methylome of nitrogen- and phosphorus-deficient maize roots by reduced representation sequencing and analyze their relationship with gene expression under prolonged stresses...
2018: Frontiers in Plant Science
Jia-Xing Yue, Gianni Liti
Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process...
June 2018: Nature Protocols
Robert A Syme, Anke Martin, Nathan A Wyatt, Julie A Lawrence, Mariano J Muria-Gonzalez, Timothy L Friesen, Simon R Ellwood
Pyrenophora teres , P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes...
2018: Frontiers in Genetics
Peng Liu, Libo Jiang, Yun Liang, Houlei Wang, Hao Zhou, Xilei Li, Hong Lin, Xiaogang Zhou, Jian Dong
OBJECTIVE: Due to radical resection, total en-bloc spondylectomy (TES) is associated with significant levels of surgical injury and spinal instability, particularly in elderly patients with solitary spinal metastases (SM), whether the possible benefits outweigh the risk requires intense consideration. Our aim was to compare and analyze the impact of age on patient prognosis. PATIENTS AND METHODS: This study investigated TES in 78 consecutive patients with solitary SM, who were divided into Group A (>65 years, n = 32) and group B (<60 years of age, n = 46)...
April 3, 2018: Clinical Neurology and Neurosurgery
Mohammad M Pourseif, Gholamali Moghaddam, Hossein Daghighkia, Ahmad Nematollahi, Yadollah Omidi
Introduction: In this study, we targeted the worm stage of Echinococcus granulosus to design a novel multi-epitope B- and helper T-cell based vaccine construct for immunization of dogs against this multi-host parasite. Methods: The vaccine was designed based on the local Eg14-3-3 antigen (Ag). DNA samples were extracted from the protoscoleces of the infected sheep's liver, and then subjected to the polymerase chain reaction (PCR) with 14-3-3 specific forward and reverse primers. For the vaccine designing, several in silico steps were undertaken...
2018: BioImpacts: BI
Robert Kofler, Kirsten-André Senti, Viola Nolte, Ray Tobler, Christian Schlötterer
The first tracking of the dynamics of a natural invasion by a transposable element (TE) provides unprecedented details on the establishment of host defense mechanisms against TEs. We captured a D. simulans population at an early stage of a P - element invasion and studied the spread of the TE in replicated experimentally evolving populations kept under hot and cold conditions. We analyzed the factors controlling the invasion by NGS, RNA-FISH, and gonadal dysgenesis assays. Under hot conditions, the P - element spread rapidly for 20 generations, but no further spread was noted later on...
April 30, 2018: Genome Research
Lu Zeng, Stephen M Pederson, Danfeng Cao, Zhipeng Qu, Zhiqiang Hu, David L Adelson, Chaochun Wei
Nearly half of the human genome is made up of transposable elements (TEs), and there is evidence that TEs are involved in gene regulation. In this study, we have integrated publicly available genomic, epigenetic, and transcriptomic data to investigate this in a genome-wide manner. A bootstrapping statistical method was applied to minimize confounder effects from different repeat types. Our results show that although most TE classes are primarily associated with reduced gene expression, Alu elements are associated with upregulated gene expression...
April 30, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Sophie Lanciano, Marie Mirouze
Transposable elements (TEs) were first identified through the polymorphisms they induced in plants and animals. Genomic studies have later revealed that TEs were highly abundant in eukaryotic genomes. Recently, more precise single individual genomic analyses have unravelled the huge diversity of TE insertions in many plant and animal species. In most cases the stress conditions behind this diversity are not known and neither is the adaptive capacity of these natural TE-induced variants. Here, we review some of the most recent examples of TE-related impacts on gene expression at the locus or the genome level and discuss the rich diversity of the TE repertoire and its potential role in adaptive evolution...
April 26, 2018: Current Opinion in Genetics & Development
Shinya Fukuda, Tetsuya Hirata, Kazuaki Neriishi, Akari Nakazawa, Masashi Takamura, Gentaro Izumi, Miyuki Harada, Yasushi Hirota, Kaori Koga, Osamu Wada-Hiraike, Tomoyuki Fujii, Yutaka Osuga
OBJECTIVES: To evaluate the clinical features of thoracic endometriosis syndrome (TES) represented by catamenial pneumothorax (CP), endometriosis-related pneumothorax (ERP), and catamenial hemoptysis (CH). STUDY DESIGN: In this retrospective study, we enrolled 25 patients with TES, 18 of whom had CP/ERP and 7 had CH, to investigate the clinical presentation, effectiveness of treatment, and recurrence rates in these disorders. RESULTS: The age at onset was significantly lower in patients with CH than in patients with CP/ERP (P < 0...
April 20, 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
Wei-Yih Chiu, Wei-Shiung Yang, Jung-Yien Chien, Jang-Jaer Lee, Keh-Sung Tsai
BACKGROUND: Although bisphosphonate-related osteonecrosis of the jaw (ONJ) develops mainly after tooth extractions (TEs), the strength of the association between them and how the existence of the disease among bisphosphonate (BP)-treated osteoporotic patients exposed to TE remain uncertain. METHODS: A nationwide retrospective cohort study investigated the influence of alendronate and TE on the development of ONJ. RESULTS: Incidence of ONJ following long-term alendronate therapy was 262/100,000 person-years, while no event developed in the control group on raloxifene...
2018: PloS One
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