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repetitive elements

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https://www.readbyqxmd.com/read/28721856/repeat-induced-point-mutation-and-other-genome-defense-mechanisms-in-fungi
#1
Eugene Gladyshev
Transposable elements have colonized the genomes of nearly all organisms, including fungi. Although transposable elements may sometimes provide beneficial functions to their hosts their overall impact is considered deleterious. As a result, the activity of transposable elements needs to be counterbalanced by the host genome defenses. In fungi, the primary genome defense mechanisms include repeat-induced point mutation (RIP) and methylation induced premeiotically, meiotic silencing by unpaired DNA, sex-induced silencing, cosuppression (also known as somatic quelling), and cotranscriptional RNA surveillance...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28716432/effect-of-frequency-and-focal-spacing-on-transcranial-histotripsy-clot-liquefaction-using-electronic-focal-steering
#2
Tyler Gerhardson, Jonathan R Sukovich, Aditya S Pandey, Timothy L Hall, Charles A Cain, Zhen Xu
This in vitro study investigated the effects of ultrasound frequency and focal spacing on blood clot liquefaction via transcranial histotripsy. Histotripsy pulses were delivered using two 256-element hemispherical transducers of different frequency (250 and 500 kHz) with 30-cm aperture diameters. A 4-cm diameter spherical volume of in vitro blood clot was treated through 3 excised human skullcaps by electronically steering the focus with frequency proportional focal spacing: λ/2, 2 λ/3 and λ with 50 pulses per location...
July 14, 2017: Ultrasound in Medicine & Biology
https://www.readbyqxmd.com/read/28714743/an-alternate-test-of-tackling-ability-in-rugby-league-players
#3
Michael J A J Speranza, Tim J Gabbett, David A Greene, Rich D Johnston, Andrew D Townshend, Brett O'Farrell
This study investigated the relationship between two tests of tackling ability, muscular strength and power in semi-professional rugby league players. Thirty-one players, 19 first grade and 12 second grade underwent tests of muscular strength (1 repetition maximum bench press, chin-up, and squat) and power (plyometric push-up and countermovement jump). Tackling ability was assessed via video analysis of under-the-ball and over-the-ball tackle drills. The first grade players had significantly greater scores in both the under-the-ball (P = 0...
July 17, 2017: International Journal of Sports Physiology and Performance
https://www.readbyqxmd.com/read/28705201/genotypic-diversity-among-multidrug-resistant-pseudomonas-aeruginosa-and-acinetobacter-species-at-mulago-hospital-in-kampala-uganda
#4
David P Kateete, Ritah Nakanjako, Moses Okee, Moses L Joloba, Christine F Najjuka
BACKGROUND: Multidrug resistant Pseudomonas aeruginosa and Acinetobacter species are common causes of nosocomial infections worldwide. Recently we reported the occurrence of carbapenem resistant Enterobacteriaceae, P. aeruginosa and Acinetobacter species at Mulago National Referral Hospital in Kampala, Uganda, but the isolates were not analyzed for genetic relatedness. Herein we report the intra-species genotypic diversity among P. aeruginosa and Acinetobacter baumannii isolated from hospitalized patients and the environment at Mulago Hospital, using repetitive elements-based PCR (Rep-PCR) genotyping...
July 14, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28704058/elucidating-protein-dna-interactions-in-human-alphoid-chromatin-via-hybridization-capture-and-mass-spectrometry
#5
Katherine E Buxton, Julia Kennedy-Darling, Michael R Shortreed, Nur Zafirah Zaidan, Michael Olivier, Mark Scalf, Rupa Sridharan, Lloyd M Smith
The centromere is the chromosomal locus where the kinetochore forms, and is critical for ensuring proper segregation of sister chromatids during cell division. A substantial amount of effort has been devoted to understanding the characteristic features and roles of the centromere, yet some fundamental aspects of the centromere, such as the complete list of elements that define it, remain obscure. It is well known that human centromeres include a highly repetitive class of DNA known as alpha satellite, or alphoid, DNA...
July 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28696511/direct-application-of-rep-pcr-on-type-i-sourdough-matrix-to-monitor-the-dominance-and-persistence-of-a-lactobacillus-plantarum-starter-throughout-back-slopping
#6
Paola Dolci, Luca Cocolin
This study describes the optimization and application of repetitive element-PCR (rep-PCR) technique directly on microbial DNA extracted from type I sourdoughs for fast monitoring of a Lb. plantarum starter strain (P1FMC) throughout daily back-slopping. The challenge was to follow and study the performance of a starter culture directly in sourdoughs without cultivation on selective media. The extraction of good quality microbial DNA suitable for amplification from a complex matrix such as dough was the first target...
July 11, 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28693467/predicting-rna-hyper-editing-with-a-novel-tool-when-unambiguous-alignment-is-impossible
#7
Wilson H McKerrow, Yiannis A Savva, Ali Rezaei, Robert A Reenan, Charles E Lawrence
BACKGROUND: Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations...
July 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28692668/a-novel-species-specific-real-time-pcr-assay-for-the-detection-of-the-emerging-zoonotic-parasite-ancylostoma-ceylanicum-in-human-stool
#8
Marina Papaiakovou, Nils Pilotte, Jessica R Grant, Rebecca J Traub, Stacey Llewellyn, James S McCarthy, Alejandro J Krolewiecki, Rubén Cimino, Rojelio Mejia, Steven A Williams
BACKGROUND: Molecular-based surveys have indicated that Ancylostoma ceylanicum, a zoonotic hookworm, is likely the second most prevalent hookworm species infecting humans in Asia. Most current PCR-based diagnostic options for the detection of Ancylostoma species target the Internal Transcribed Spacer (ITS) regions of the ribosomal gene cluster. These regions possess a considerable degree of conservation among the species of this genus and this conservation can lead to the misidentification of infecting species or require additional labor for accurate species-level determination...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28688040/identification-of-all-homoeologous-chromosomes-of-newly-synthetic-allotetraploid-cucumis-%C3%A3-hytivus-and-its-wild-parent-reveals-stable-subgenome-structure
#9
Yunzhu Wang, Qinzheng Zhao, Xiaodong Qin, Shuqiong Yang, Ziang Li, Ji Li, Qunfeng Lou, Jinfeng Chen
Allopolyploidy and homoeologous recombination are two important processes in reshaping genomes and generating evolutionary novelties. Newly formed allopolyploids usually display chromosomal perturbations as a result of pairing errors at meiosis. To understand mechanisms of stabilization of allopolyploid species derived from distant chromosome bases, we investigated mitotic stability of a synthetic Cucumis allotetraploid species in relation to meiosis chromosome behavior. The Cucumis × hytivus is an allotetraploid synthesized from interspecific hybridization between cucumber (Cucumis sativus, 2n = 14) and its wild relative Cucumis hystrix (2n = 24) followed by spontaneous chromosome doubling...
July 7, 2017: Chromosoma
https://www.readbyqxmd.com/read/28685945/evolutionary-changes-of-hox-genes-and-relevant-regulatory-factors-provide-novel-insights-into-mammalian-morphological-modifications
#10
Kui Li, Xiaohui Sun, Meixiu Chen, Yingying Sun, Ran Tian, Zhengfei Wang, Shixia Xu, Guang Yang
The diversity of body plan of mammals accelerates the innovation of lifestyles and the extensive adaptation to different habitats, including terrestrial, aerial, and aquatic habitats. However, the genetic basis of those phenotypic modifications, which occurred during mammalian evolution, remains poorly explored. In the present study, we synthetically surveyed the evolutionary pattern of Hox clusters that played a powerful role in the morphogenesis along the head-tail axis of animal embryos and main regulatory factors (Mll, Bmi1, and E2f6) that control the expression of Hox genes...
July 7, 2017: Integrative Zoology
https://www.readbyqxmd.com/read/28682306/unique-roles-for-histone-h3k9me-states-in-rnai-and-heritable-silencing-of-transcription
#11
Gloria Jih, Nahid Iglesias, Mark A Currie, Natarajan V Bhanu, Joao A Paulo, Steven P Gygi, Benjamin A Garcia, Danesh Moazed
Heterochromatic DNA domains play important roles in regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway(1-9). Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and tri-methylation (H3K9me2 and H3K9me3, respectively) and heterochromatin formation(10-17)...
June 22, 2017: Nature
https://www.readbyqxmd.com/read/28677663/inter-strain-differences-in-line-1-dna-methylation-in-the-mouse-hematopoietic-system-in-response-to-exposure-to-ionizing-radiation
#12
Isabelle R Miousse, Jianhui Chang, Lijian Shao, Rupak Pathak, Étienne Nzabarushimana, Kristy R Kutanzi, Reid D Landes, Alan J Tackett, Martin Hauer-Jensen, Daohong Zhou, Igor Koturbash
Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons are the major repetitive elements in mammalian genomes. LINE-1s are well-accepted as driving forces of evolution and critical regulators of the expression of genetic information. Alterations in LINE-1 DNA methylation may lead to its aberrant activity and are reported in virtually all human cancers and in experimental carcinogenesis. In this study, we investigated the endogenous DNA methylation status of the 5' untranslated region (UTR) of LINE-1 elements in the bone marrow hematopoietic stem cells (HSCs), hematopoietic progenitor cells (HPCs), and mononuclear cells (MNCs) in radioresistant C57BL/6J and radiosensitive CBA/J mice and in response to ionizing radiation (IR)...
July 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28674489/multi-finger-interaction-and-synergies-in-finger-flexion-and-extension-force-production
#13
Jaebum Park, Dayuan Xu
The aim of this study was to discover finger interaction indices during single-finger ramp tasks and multi-finger coordination during a steady state force production in two directions, flexion, and extension. Furthermore, the indices of anticipatory adjustment of elemental variables (i.e., finger forces) prior to a quick pulse force production were quantified. It is currently unknown whether the organization and anticipatory modulation of stability properties are affected by force directions and strengths of in multi-finger actions...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28667019/retrotransposons-are-the-major-contributors-to-the-expansion-of-the-drosophila-ananassae-muller-f-element
#14
Wilson Leung, Christopher D Shaffer, Elizabeth J Chen, Thomas J Quisenberry, Kevin Ko, John M Braverman, Thomas C Giarla, Nathan T Mortimer, Laura K Reed, Sheryl T Smith, Srebrenka Robic, Shannon R McCartha, Danielle R Perry, Lindsay M Prescod, Zenyth A Sheppard, Ken J Saville, Allison McClish, Emily A Morlock, Victoria R Sochor, Brittney Stanton, Isaac C Veysey-White, Dennis Revie, Luis A Jimenez, Jennifer J Palomino, Melissa D Patao, Shane M Patao, Edward T Himelblau, Jaclyn D Campbell, Alexandra L Hertz, Maddison F McEvilly, Allison R Wagner, James Youngblom, Baljit Bedi, Jeffery Bettincourt, Erin Duso, Maiye Her, William Hilton, Samantha House, Masud Karimi, Kevin Kumimoto, Rebekah Lee, Darryl Lopez, George Odisho, Ricky Prasad, Holly Lyn Robbins, Tanveer Sandhu, Tracy Selfridge, Kara Tsukashima, Hani Yosif, Nighat P Kokan, Latia Britt, Alycia Zoellner, Eric P Spana, Ben T Chlebina, Insun Chong, Harrison Friedman, Danny A Mammo, Chun L Ng, Vinayak S Nikam, Nicholas U Schwartz, Thomas Q Xu, Martin G Burg, Spencer M Batten, Lindsay M Corbeill, Erica Enoch, Jesse J Ensign, Mary E Franks, Breanna Haiker, Judith A Ingles, Lyndsay D Kirkland, Joshua M Lorenz-Guertin, Jordan Matthews, Cody M Mittig, Nicholaus Monsma, Katherine J Olson, Guillermo Perez-Aragon, Alen Ramic, Jordan R Ramirez, Christopher Scheiber, Patrick A Schneider, Devon E Schultz, Matthew Simon, Eric Spencer, Adam C Wernette, Maxine E Wykle, Elizabeth Zavala-Arellano, Mitchell J McDonald, Kristine Ostby, Peter Wendland, Justin R DiAngelo, Alexis M Ceasrine, Amanda H Cox, James E B Docherty, Robert M Gingras, Stephanie M Grieb, Michael J Pavia, Casey L Personius, Grzegorz L Polak, Dale L Beach, Heaven L Cerritos, Edward A Horansky, Karim A Sharif, Ryan Moran, Susan Parrish, Kirsten Bickford, Jennifer Bland, Juliana Broussard, Kerry Campbell, Katelynn E Deibel, Richard Forka, Monika C Lemke, Marlee B Nelson, Catherine O'Keeffe, S Mariel Ramey, Luke Schmidt, Paola Villegas, Christopher J Jones, Stephanie L Christ, Sami Mamari, Adam S Rinaldi, Ghazal Stity, Amy T Hark, Mark Scheuerman, Cathy Silver Key, Briana D McRae, Adam S Haberman, Sam Asinof, Harriette Carrington, Kelly Drumm, Terrance Embry, Richard McGuire, Drew Miller-Foreman, Stella Rosen, Nadia Safa, Darrin Schultz, Matt Segal, Yakov Shevin, Petros Svoronos, Tam Vuong, Gary Skuse, Don W Paetkau, Rachael K Bridgman, Charlotte M Brown, Alicia R Carroll, Francesca M Gifford, Julie Beth Gillespie, Susan E Herman, Krystal L Holtcamp, Misha A Host, Gabrielle Hussey, Danielle M Kramer, Joan Q Lawrence, Madeline M Martin, Ellen N Niemiec, Ashleigh P O'Reilly, Olivia A Pahl, Guadalupe Quintana, Elizabeth A S Rettie, Torie L Richardson, Arianne E Rodriguez, Mona O Rodriguez, Laura Schiraldi, Joanna J Smith, Kelsey F Sugrue, Lindsey J Suriano, Kaitlyn E Takach, Arielle M Vasquez, Ximena Velez, Elizabeth J Villafuerte, Laura T Vives, Victoria R Zellmer, Jeanette Hauke, Charles R Hauser, Karolyn Barker, Laurie Cannon, Perouza Parsamian, Samantha Parsons, Zachariah Wichman, Christopher W Bazinet, Diana E Johnson, Abubakarr Bangura, Jordan A Black, Victoria Chevee, Sarah A Einsteen, Sarah K Hilton, Max Kollmer, Rahul Nadendla, Joyce Stamm, Antoinette E Fafara-Thompson, Amber M Gygi, Emmy E Ogawa, Matt Van Camp, Zuzana Kocsisova, Judith L Leatherman, Cassie M Modahl, Michael R Rubin, Susana S Apiz-Saab, Suzette M Arias-Mejias, Carlos F Carrion-Ortiz, Patricia N Claudio-Vazquez, Debbie M Espada-Green, Marium Feliciano-Camacho, Karina M Gonzalez-Bonilla, Mariela Taboas-Arroyo, Dorianmarie Vargas-Franco, Raquel Montañez-Gonzalez, Joseph Perez-Otero, Myrielis Rivera-Burgos, Francisco J Rivera-Rosario, Heather L Eisler, Jackie Alexander, Samatha K Begley, Deana Gabbard, Robert J Allen, Wint Yan Aung, William D Barshop, Amanda Boozalis, Vanessa P Chu, Jeremy S Davis, Ryan N Duggal, Robert Franklin, Katherine Gavinski, Heran Gebreyesus, Henry Z Gong, Rachel A Greenstein, Averill D Guo, Casey Hanson, Kaitlin E Homa, Simon C Hsu, Yi Huang, Lucy Huo, Sarah Jacobs, Sasha Jia, Kyle L Jung, Sarah Wai-Chee Kong, Matthew R Kroll, Brandon M Lee, Paul F Lee, Kevin M Levine, Amy S Li, Chengyu Liu, Max Mian Liu, Adam P Lousararian, Peter B Lowery, Allyson P Mallya, Joseph E Marcus, Patrick C Ng, Hien P Nguyen, Ruchik Patel, Hashini Precht, Suchita Rastogi, Jonathan M Sarezky, Adam Schefkind, Michael B Schultz, Delia Shen, Tara Skorupa, Nicholas C Spies, Gabriel Stancu, Hiu Man Vivian Tsang, Alice L Turski, Rohit Venkat, Leah E Waldman, Kaidi Wang, Tracy Wang, Jeffrey W Wei, Dennis Y Wu, David D Xiong, Jack Yu, Karen Zhou, Gerard P McNeil, Robert W Fernandez, Patrick Gomez Menzies, Tingting Gu, Jeremy Buhler, Elaine R Mardis, Sarah C R Elgin
The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (~5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in Drosophila ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4 Mb region of the D. ananassae F element, and a 1.7 Mb region from the D element for comparison...
June 30, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28659711/conservation-of-repeats-at-the-mammalian-kcnq1ot1-cdkn1c-region-suggests-a-role-in-genomic-imprinting
#15
Marcos De Donato, Tanveer Hussain, Hectorina Rodulfo, Sunday O Peters, Ikhide G Imumorin, Bolaji N Thomas
KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS), but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements), compared with their whole chromosomes (detected by RepeatMasker)...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28654059/comprehensive-dna-methylation-analysis-using-a-methyl-cpg-binding-domain-capture-based-method-in-chronic-lymphocytic-leukemia-patients
#16
Santhilal Subhash, Meena Kanduri
The role of long noncoding RNAs (lncRNAs) in cancer is coming to the forefront due to growing interest in understanding their mechanistic functions during cancer development and progression. Despite this, the global epigenetic regulation of lncRNAs and repetitive sequences in cancer has not been well investigated, particularly in chronic lymphocytic leukemia (CLL). This study focuses on a unique approach: the immunoprecipitation-based capture of double-stranded, methylated DNA fragments using methyl-binding domain (MBD) proteins, followed by next-generation sequencing (MBD-seq)...
June 16, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28653298/two-new-miniature-inverted-repeat-transposable-elements-in-the-genome-of-the-clam-donax-trunculus
#17
Eva Šatović, Miroslav Plohl
Repetitive sequences are important components of eukaryotic genomes that drive their evolution. Among them are different types of mobile elements that share the ability to spread throughout the genome and form interspersed repeats. To broaden the generally scarce knowledge on bivalves at the genome level, in the clam Donax trunculus we described two new non-autonomous DNA transposons, miniature inverted-repeat transposable elements (MITEs), named DTC M1 and DTC M2. Like other MITEs, they are characterized by their small size, their A + T richness, and the presence of terminal inverted repeats (TIRs)...
June 26, 2017: Genetica
https://www.readbyqxmd.com/read/28648762/repetitive-deliberate-fires-development-and-validation-of-a-methodology-to-detect-series
#18
Eva Bruenisholz, Olivier Delémont, Olivier Ribaux, Linzi Wilson-Wilde
The detection of repetitive deliberate fire events is challenging and still often ineffective due to a case-by-case approach. A previous study provided a critical review of the situation and analysis of the main challenges. This study suggested that the intelligence process, integrating forensic data, could be a valid framework to provide a follow-up and systematic analysis provided it is adapted to the specificities of repetitive deliberate fires. In this current manuscript, a specific methodology to detect deliberate fires series, i...
June 16, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28641941/role-of-recombination-and-replication-fork-restart-in-repeat-instability
#19
REVIEW
Erica J Polleys, Nealia C M House, Catherine H Freudenreich
Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28639668/a-strategy-for-fabrication-of-controllable-3d-pattern-containing-clusters-and-nanoparticles-inside-a-solid-material
#20
Qiuqun Chen, Hui Song, Fangteng Zhang, Hang Zhang, Yongze Yu, Zhi Chen, Rongfei Wei, Ye Dai, Jianrong Qiu
Directly controlling the growth process of clusters and nanoparticles is an effective way to tune their specific properties, which has been considered as a significant issue lying at the heart of nanotechnology. For technological applications, great strides have been made in the assembly of clusters and nanoparticles. However, controllable synthesis of clusters and nanoparticles inside a bulk solid-state medium remains a tremendous challenge, which is important for integrated devices. Here we report a strategy for space-selective control of elemental tellurium (Te) precipitation as clusters or nanoparticles in glass by femtosecond (fs) laser irradiation...
July 6, 2017: Nanoscale
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