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https://www.readbyqxmd.com/read/29445022/whole-genome-duplication-and-transposable-element-proliferation-drive-genome-expansion-in-corydoradinae-catfishes
#1
Sarah Marburger, Markos A Alexandrou, John B Taggart, Simon Creer, Gary Carvalho, Claudio Oliveira, Martin I Taylor
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size-0...
February 14, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29440596/multi-omics-driven-assembly-and-annotation-of-the-sandalwood-santalum-album-genome
#2
H B Mahesh, Pratigya Subba, Jayshree Advani, Meghana Deepak Shirke, Ramya Malarini Loganathan, S Chandana, S Shilpa, Oishi Chatterjee, Sneha M Pinto, Keshava Prasad, Malali Gowda
Santalum album (Indian sandalwood) is an important tropical evergreen tree, known for its fragrant heartwood-derived essential oil and its valuable carving wood. Here, we applied an integrated genomic, transcriptomic, and proteomic approach to assemble and annotate the Indian sandalwood genome. Our genome sequencing resulted in the establishment of a draft map of the smallest genome for any woody tree species to date (221 Mb). The genome annotation predicted 38,119 protein-coding genes and 27.42% repetitive DNA elements...
February 12, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29440567/cellular-and-molecular-mechanisms-of-centromere-drive
#3
Michael A Lampson, Ben E Black
The asymmetric outcome of female meiosis I, whereby an entire set of chromosomes are discarded into a polar body, presents an opportunity for selfish genetic elements to cheat the process and disproportionately segregate to the egg. Centromeres, the chromosomal loci that connect to spindle microtubules, could potentially act as selfish elements and "drive" in meiosis. We review the current understanding of the genetic and epigenetic contributions to centromere identity and describe recent progress in a powerful model system to study centromere drive in mice...
February 12, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29439662/comparative-genome-analysis-of-52-fish-species-suggests-differential-associations-of-repetitive-elements-with-their-living-aquatic-environments
#4
Zihao Yuan, Shikai Liu, Tao Zhou, Changxu Tian, Lisui Bao, Rex Dunham, Zhanjiang Liu
BACKGROUND: Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. RESULTS: The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29426222/gemas-cns-concentrations-and-c-n-ratios-in-european-agricultural-soil
#5
Jörg Matschullat, Clemens Reimann, Manfred Birke, Debora Dos Santos Carvalho
A reliable overview of measured concentrations of TC, TN and TS, TOC/TN ratios, and their regional distribution patterns in agricultural soil at the continental scale and based on measured data has been missing - despite much previous work on local and the European scales. Detection and mapping of natural (ambient) background element concentrations and variability in Europe was the focus of this work. While total C and S data had been presented in the GEMAS atlas already, this work delivers more precise (lower limit of determination) and fully quantitative data, and for the first time high-quality TN data...
February 5, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29425140/an-experimental-exploration-of-the-effects-of-exposure-to-images-of-nature-on-rumination
#6
Sarah Elizabeth Golding, Birgitta Gatersleben, Mark Cropley
Exposure to natural environments has been shown to have beneficial effects on mood. Rumination is a thinking style associated with negative mood, and sometimes depression, and is characterized by repetitive, intrusive thoughts, often with a negative emotional element. This study investigated whether exposure to nature, operationalized using photographs presented as a slideshow, could aid reduction in levels of state rumination. An experimental, within-between (Time x Condition) participant design was used; participants (n = 58) undertook a presentation task designed to induce rumination and influence mood...
February 9, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29424472/characterization-of-a-satellite-dna-in-the-genera%C3%A2-lacerta%C3%A2-and-timon-reptilia-lacertidae-and-its-role-in-the-differentiation-of-the-w-chromosome
#7
Massimo Giovannotti, Paola Nisi Cerioni, Verónica Rojo, Ettore Olmo, Tahar Slimani, Andrea Splendiani, Vincenzo Caputo Barucchi
In this study, IMO-TaqI satDNA, previously isolated in several species of Lacertidae, was isolated and characterized from four species of the genus Lacerta and three of the genus Timon. The aim was to gain further insights into the evolutionary dynamics of this satDNA, its occurrence among lacertids and to understand if it plays any role in sex chromosome evolution in these seven species. The results here obtained highlighted the presence of this repetitive element in the genome of all the species investigated, thus indicating that IMO-TaqI satDNA is evolutionary conserved among a wide variety of lacertids...
February 9, 2018: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/29423997/draft-genome-sequence-of-ramie-boehmeria-nivea-l-gaudich
#8
Ming-Bao Luan, Jian-Bo Jian, Ping Chen, Jun-Hui Chen, Jian-Hua Chen, Qiang Gao, Gang Gao, Ju-Hong Zhou, Kun-Mei Chen, Xuan-Min Guang, Ji-Kang Chen, Qian-Qian Zhang, Xiao-Fei Wang, Long Fang, Zhi-Min Sun, Ming-Zhou Bai, Xiao-Dong Fang, Shan-Cen Zhao, He-Ping Xiong, Chun-Ming Yu, Ai-Guo Zhu
Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fiber crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fiber quality, protein content, and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach...
February 8, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29421973/multimodal-characterization-of-the-late-effects-of-tbi-letbi-a-methodological-overview-of-the-letbi-project
#9
Brian L Edlow, C Dirk Keene, Daniel Perl, Diego Iacono, Rebecca Folkerth, William Stewart, Christine L MacDonald, Jean Augustinack, Ramon Diaz-Arrastia, Camilo Estrada, Elissa Flannery, Wayne Gordon, Tom Grabowski, Kelly Hansen, Jeanne Hoffman, Christopher Kroenke, Eric Larson, Patricia Lee, Azma Mareyam, Jennifer A McNab, Jeanne McPhee, Allison L Moreau, Anne Renz, KatieRose Richmire, Allison Stevens, Cheuk Y Tang, Lee S Tirrell, Emily Trittschuh, Andre van der Kouwe, Ani Varjabedian, Lawrence L Wald, Ona Wu, Anastasia Yendiki, Liza Young, Lilla Zollei, Bruce Fischl, Paul K Crane, Kristen Dams-O'Connor
Epidemiological studies suggest that a single moderate-to-severe traumatic brain injury (TBI) is associated with an increased risk of neurodegenerative disease, including Alzheimer's and Parkinson's disease (AD and PD). Histopathological studies describe complex neurodegenerative pathologies in individuals exposed to single moderate-to-severe TBI or repetitive mild TBI, including chronic traumatic encephalopathy (CTE). However, the clinicopathological links between TBI and post-traumatic neurodegenerative diseases such as AD, PD, and CTE remain poorly understood...
February 8, 2018: Journal of Neurotrauma
https://www.readbyqxmd.com/read/29409498/dna-methylome-profiling-at-single-base-resolution-through-bisulfite-sequencing-of-5mc-immunoprecipitated-dna
#10
Zhen Jia, Yueyi Shi, Lei Zhang, Yipeng Ren, Tong Wang, Lejun Xing, Baorong Zhang, Guolan Gao, Rongfa Bu
BACKGROUND: Detection of DNA methylome at single-base resolution is a significant challenge but promises to shed considerable light on human disease etiology. Current technologies could not detect DNA methylation genome-wide at single-base resolution with small amount of sequencing data and could not avoid detecting the methylation of repetitive elements which are considered as "junk DNA". METHODS: In this study, we have developed a novel DNA methylome profiling technology named MB-seq with its ability to identify genome-wide 5mC and quantify DNA methylation levels by introduced an assistant adapter AluI-linker This linker can be ligated to sonicated DNA and then be digested after the bisulfite treatment and amplification, which has no effect of MeDIP enrichment...
February 6, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/29405025/-applying-game-based-learning-in-nursing-education-empathy-board-game-learning
#11
Chueh-Fen Lu, Shu-Mei Wu, Ying-Mei Shu, Mei-Yu Yeh
Attending lectures and reading are two common approaches to acquiring knowledge, while repetitive practice is a common approach to acquiring skills. Nurturing proper attitudes in students is one of the greatest challenges for educators. Health professionals must incorporate empathy into their practice. Creative teaching strategies may offer a feasible approach to enhancing empathy-related competence. The present article focuses on analyzing current, empathy-related curriculums in nursing education in Taiwan, exploring the concepts of empathy and game-based learning, presenting the development of an empathy board game as a teaching aid, and, finally, evaluating the developed education application...
February 2018: Hu Li za Zhi the Journal of Nursing
https://www.readbyqxmd.com/read/29401301/single-molecule-real-time-smrt-sequencing-comes-of-age-applications-and-utilities-for-medical-diagnostics
#12
Simon Ardui, Adam Ameur, Joris R Vermeesch, Matthew S Hestand
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems...
February 1, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29400649/train-transcription-of-repeats-activates-interferon-in-response-to-chromatin-destabilization-induced-by-small-molecules-in-mammalian-cells
#13
Katerina Leonova, Alfiya Safina, Elimelech Nesher, Poorva Sandlesh, Rachel Pratt, Catherine Burkhart, Brittany Lipchick, Ilya Gitlin, Costakis Frangou, Igor Koman, Jianmin Wang, Kirill Kirsanov, Marianna G Yakubovskaya, Andrei V Gudkov, Katerina Gurova
Cellular Responses to the loss of genomic stability are well-established, while how mammalian cells respond to chromatin destabilization is largely unknown. We previously found that DNA demethylation on p53-deficient background leads to transcription of repetitive heterochromatin elements, followed by an interferon response, a phenomenon we named TRAIN (Transcription of Repeats Activates INterferon). Here, we report that curaxin, an anticancer small molecule, destabilizing nucleosomes via disruption of histone/DNA interactions, also induces TRAIN...
February 5, 2018: ELife
https://www.readbyqxmd.com/read/29397462/molecular-testing-of-klebsiella-pneumoniae-contaminating-tissue-allografts-recovered-from-deceased-donors
#14
Zohreh Ghalavand, Alireza Heidary Rouchi, Hassan Bahraminasab, Elham Ravanasa, Elnaz Sadat Mirsamadi, Narges Nodeh Farahani, Bahram Nikmanesh
Microbiological screening of tissue allografts is crucial to prevent the transmission of bacterial and fungal infections to transplant recipients. Klebsiella was the most prevalent and resistant contaminating microorganism observed in our setting in the Iranian Tissue Bank. This study was conducted to determine the presence of extended-spectrum β-lactamase (ESBL) genes, antimicrobial resistance patterns of Klebsiella pneumoniae isolates, and their clonal relationships in allograft materials. K. pneumoniae contaminating bone and other tissue allografts recovered from deceased donors were identified and ESBL isolates were detected using a phenotypic confirmatory method...
February 3, 2018: Cell and Tissue Banking
https://www.readbyqxmd.com/read/29393586/population-structure-and-antimicrobial-susceptibility-of-paenibacillus-larvae-isolates-from-american-foulbrood-cases-in-apis-mellifera-in-japan
#15
Yuichi Ueno, Emi Yoshida, Wakako Misumi, Eri Watando, Kenta Suzuki, Yuko Hirai, Masatoshi Okura, Makoto Osaki, Ken Katsuda, Daisuke Takamatsu
Paenibacillus larvae is the causative agent of American foulbrood (AFB), the most destructive disease of the honey bee brood. In this study, we investigated the population structure and antimicrobial susceptibility of Japanese P. larvae using 100 isolates isolated between 1993 and 2017 in 17 prefectures. Using repetitive-element PCR and multilocus sequence typing, isolates from diverse origins were classified into six genotypes, including the novel genotype ERIC II-ST24. Among these genotypes, ERIC I-ST15 is the most common in Japan, while ERIC II-ST10 isolates were found to be increasing during the 2010s...
February 2, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29393154/long-interspersed-element-1-methylation-level-as-a-prognostic-biomarker-in-gastrointestinal-cancers
#16
Yoshifumi Baba, Taisuke Yagi, Hiroshi Sawayama, Yukiharu Hiyoshi, Takatsugu Ishimoto, Masaaki Iwatsuki, Yuji Miyamoto, Naoya Yoshida, Hideo Baba
Epigenetic changes play a crucial role in human cancer development. DNA methylation is a central epigenetic process that regulates levels of gene expression. Changes in DNA methylation that occur in human tumors include global DNA hypomethylation and site-specific CpG island promoter hypermethylation. Long interspersed element-1 (LINE-1) is a repetitive DNA retrotransposon that duplicates via a copy-and-paste genetic mechanism. As LINE-1 constitutes approximately 17% of the human genome, the extent of LINE-1 methylation is regarded as a surrogate marker of global DNA methylation...
February 1, 2018: Digestion
https://www.readbyqxmd.com/read/29386330/sam68-is-required-for-regulation-of-pumilio-by-the-norad-long-noncoding-rna
#17
Ailone Tichon, Rotem Ben-Tov Perry, Lovorka Stojic, Igor Ulitsky
The number of known long noncoding RNA (lncRNA) functions is rapidly growing, but how those functions are encoded in their sequence and structure remains poorly understood. NORAD (noncoding RNA activated by DNA damage) is a recently characterized, abundant, and highly conserved lncRNA that is required for proper mitotic divisions in human cells. NORAD acts in the cytoplasm and antagonizes repressors from the Pumilio family that bind at least 17 sites spread through 12 repetitive units in NORAD sequence. Here we study conserved sequences in NORAD repeats, identify additional interacting partners, and characterize the interaction between NORAD and the RNA-binding protein SAM68 (KHDRBS1), which is required for NORAD function in antagonizing Pumilio...
January 31, 2018: Genes & Development
https://www.readbyqxmd.com/read/29382748/correction-for-noh-et-al-atrx-tolerates-activity-dependent-histone-h3-methyl-phos-switching-to-maintain-repetitive-element-silencing-in-neurons
#18
(no author information available yet)
No abstract text is available yet for this article.
January 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29380046/low-pass-single-chromosome-sequencing-of-human-small-supernumerary-marker-chromosomes-ssmcs-and-apodemus-b-chromosomes
#19
Alexey I Makunin, Marija Rajičić, Tatyana V Karamysheva, Svetlana A Romanenko, Anna S Druzhkova, Jelena Blagojević, Mladen Vujošević, Nikolay B Rubtsov, Alexander S Graphodatsky, Vladimir A Trifonov
Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes...
January 30, 2018: Chromosoma
https://www.readbyqxmd.com/read/29378810/repressive-chromatin-in-caenorhabditis-elegans-establishment-composition-and-function
#20
Julie Ahringer, Susan M Gasser
Chromatin is organized and compacted in the nucleus through the association of histones and other proteins, which together control genomic activity. Two broad types of chromatin can be distinguished: euchromatin, which is generally transcriptionally active, and heterochromatin, which is repressed. Here we examine the current state of our understanding of repressed chromatin in Caenorhabditis elegans, focusing on roles of histone modifications associated with repression, such as methylation of histone H3 lysine 9 (H3K9me2/3) or the Polycomb Repressive Complex 2 (MES-2/3/6)-deposited modification H3K27me3, and on proteins that recognize these modifications...
February 2018: Genetics
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