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Relevant bibliographies by topics / Repetitive element

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Academic literature on the topic 'Repetitive element'

Author: Grafiati

Published: 14 March 2023

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Journal articles on the topic "Repetitive element"

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Gurjia, Aesha Adnan, and Ahmed Abdulwahid Dhannoon. "REPETITIVE ELEMENTS AND THEIR OBJECTIVES IN ANCIENT AND CONTEMPORARY MOSQUES." Journal of Islamic Architecture 6, no. 4 (December 26, 2021): 264–76. http://dx.doi.org/10.18860/jia.v6i4.11718.

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Mosques are the most important buildings in Islamic architectures. They represent the place of worship for Muslims. Like other architectural buildings, they consist of components and repeated elements forming their general structures. However, some of these formal elements have changed due to the mosque development and the contemporary trends. Therefore, this research was conducted to discover the repetitive use of the elements and the differences between ancient and contemporary mosques by studying ten samples of mosques. It showed the difference between these two periods in terms of element repetition and utilization. Moreover, it tried to find the related objectives of repetitive use within these two periods. It concluded that some elements from the ancient period were used repetitively in the contemporary mosques. Based on the analysis findings, the design objective is achieved by the repetitive use in both periods. Furthermore, the repetitive use of the elements as structural objective takes second place in ancient mosques. Meanwhile, the environmental objective is second to achieve in contemporary mosques.

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Cramton, Sarah E., Norbert F. Schnell, Friedrich Götz, and Reinhold Brückner. "Identification of a New Repetitive Element inStaphylococcus aureus." Infection and Immunity 68, no. 4 (April 1, 2000): 2344–48. http://dx.doi.org/10.1128/iai.68.4.2344-2348.2000.

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ABSTRACT The Staphylococcus aureus repeat (STAR) element is a sequence identified in two intergenic regions in S. aureus. The element is found in 13 to 21 copies in individual S. aureus strains, and elements in the homologous intergenic location are variable in length. The element sequence consists of several small and unusually GC-rich direct repeats with recurring intervening sequences. In addition, STAR-like elements may be present in related staphylococcal species.

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Abuín, M., P. Martínez, L. Sánchez, C. Clabby, F. Flavin, N. P. Wilkins, J. A. Houghton, R. Powell, and U. Goswami. "A NOR-associated repetitive element present in the genome of two Salmo species (salmo salar and Salmo trutta)." Genome 39, no. 4 (August 1, 1996): 671–79. http://dx.doi.org/10.1139/g96-085.

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A repetitive element was isolated from the genome of Atlantic salmon. Nucleotide sequence analysis revealed the existence of variant monomers that range in length from approximately 200 to 230 bp. Repeat monomers contain regions of cryptic simplicity, internal repetition, and long direct repeats with deletions and insertions between individual units. The repetitive element was shown to have a tandem unit arrangement and was estimated to occupy between two and three percent of the Atlantic salmon genome. Southern blot analysis revealed the repetitive element to be unique to Atlantic salmon and brown trout species. In situ hybridization analysis showed this element to be localized at the main nucleolar organizer region bearing chromosomes of Atlantic salmon (Salmo salar), AS cell line (derived from S. salar), and brown trout (Salmo trutta). Key words : Atlantic salmon, brown trout, AS cell line, repeat DNA, NOR.

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Douville, Christopher, Joshua D. Cohen, Janine Ptak, Maria Popoli, Joy Schaefer, Natalie Silliman, Lisa Dobbyn, et al. "Assessing aneuploidy with repetitive element sequencing." Proceedings of the National Academy of Sciences 117, no. 9 (February 19, 2020): 4858–63. http://dx.doi.org/10.1073/pnas.1910041117.

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We report a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) that can detect aneuploidy in samples containing as little as 3 pg of DNA. Using a single primer pair, we amplified ∼350,000 amplicons distributed throughout the genome. Aneuploidy was detected in 49% of liquid biopsies from a total of 883 nonmetastatic, clinically detected cancers of the colorectum, esophagus, liver, lung, ovary, pancreas, breast, or stomach. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% in these eight cancer types, while only 1% of 812 healthy controls scored positive.

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Foster, E., J. Hattori, P. Zhang, H. Labbé, T. Martin-Heller, J. Li-Pook-Than, T. Ouellet, K. Malik, and B. Miki. "The new RENT family of repetitive elements in Nicotiana species harbors gene regulatory elements related to the tCUP cryptic promoter." Genome 46, no. 1 (February 1, 2003): 146–55. http://dx.doi.org/10.1139/g02-102.

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The tCUP cryptic constitutive promoter was discovered in the tobacco genome by T-DNA (transfer DNA) tagging with a promoterless GUSnos gene. Here, we show that the portion of the tCUP sequence containing a variety of cryptic gene regulatory elements is related to a new family of moderately repetitive sequences (102 copies), the RENT (repetitive element from Nicotiana tabacum) family. The RENT family is found only in certain Nicotiana species. Five RENT elements were cloned and sequenced. The RENT elements are a minimum of 5 kb in length and share 8090% sequence similarity throughout their length. The 5' termini are the same in the isolated RENT family members and are characterized by a conserved border sequence (TGTTGA(T or C)ACCCAATTTT(T or C)). The 3' ends of RENT sequence similarity vary in location and sequence. The tCUP cryptic promoter originated from a unique truncated RENT element that interrupts a phytochelatin synthase-like gene that may have undergone rearrangements prior to or resulting from T-DNA insertion. No evidence was found for expressed coding regions within the RENT elements; however, like the cryptic gene regulatory elements within the tCUP sequence, the isolated RENT elements possess promoter activity and translational enhancer activity.Key words: cryptic promoter, Nicotiana, T-DNA, translational enhancer, repetitive element.

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Youssoufian, H., and H. F. Lodish. "Transcriptional inhibition of the murine erythropoietin receptor gene by an upstream repetitive element." Molecular and Cellular Biology 13, no. 1 (January 1993): 98–104. http://dx.doi.org/10.1128/mcb.13.1.98-104.1993.

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Transcription of the murine erythropoietin receptor (EpoR) gene is inhibited by a novel repetitive element that is located upstream of the EpoR promoter. Reporter gene studies reveal that the inhibitory effect is both distance and orientation dependent. This element is a member of a family of repetitive elements specific to rodents and is present at approximately 10(5) copies per mouse genome. It encodes approximately 500- to 900-bp-long transcripts in both erythroid and nonerythroid cells. RNase protection analysis with a probe from the 5' flanking murine EpoR gene reveals that the direction of transcription is in the sense orientation, relative to the downstream EpoR gene. We suggest that transcriptional inhibition of the EpoR promoter is mediated by read-through transcripts originating in the upstream repetitive element and that this effect may contribute to the basal level of transcription of the murine EpoR gene in erythroid cells.

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Youssoufian, H., and H. F. Lodish. "Transcriptional inhibition of the murine erythropoietin receptor gene by an upstream repetitive element." Molecular and Cellular Biology 13, no. 1 (January 1993): 98–104. http://dx.doi.org/10.1128/mcb.13.1.98.

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Transcription of the murine erythropoietin receptor (EpoR) gene is inhibited by a novel repetitive element that is located upstream of the EpoR promoter. Reporter gene studies reveal that the inhibitory effect is both distance and orientation dependent. This element is a member of a family of repetitive elements specific to rodents and is present at approximately 10(5) copies per mouse genome. It encodes approximately 500- to 900-bp-long transcripts in both erythroid and nonerythroid cells. RNase protection analysis with a probe from the 5' flanking murine EpoR gene reveals that the direction of transcription is in the sense orientation, relative to the downstream EpoR gene. We suggest that transcriptional inhibition of the EpoR promoter is mediated by read-through transcripts originating in the upstream repetitive element and that this effect may contribute to the basal level of transcription of the murine EpoR gene in erythroid cells.

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Marszałek, Jerzy, Jacek Stadnicki, and Piotr Danielczyk. "Finite element model of laminate construction element with multi-phase microstructure." Science and Engineering of Composite Materials 27, no. 1 (December 3, 2020): 405–14. http://dx.doi.org/10.1515/secm-2020-0044.

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AbstractThe article describes a method of creating a mesoscale finite element model of a fabric reinforced laminate that replicates the smallest repetitive fragment of its microstructure – RUC (Repetitive Unit Cell). The model takes into account the influence of the number and orientation of layers, the weave of the reinforcement fabric as well as manufacturing technology on the strength and stiffness of the laminate. The constants of the finite elements forming RUC (equivalent cross-sectional parameters, limit values of forces ensuring layer integrity) are determined experimentally by performing uncomplicated tests of specimens of a particular laminate. A special preprocessor was developed to generate the finite element model of the construction element from laminate, which automatically creates the so-called batch file defining the model. The usefulness of the preprocessor was checked by simulating a three-point bending test of a laminate door beam of a passenger car. The obtained calculation results were verified experimentally.

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Lunyak, Victoria V., and Michelle Atallah. "Genomic relationship between SINE retrotransposons, Pol III–Pol II transcription, and chromatin organization: the journey from junk to jewel." Biochemistry and Cell Biology 89, no. 5 (October 2011): 495–504. http://dx.doi.org/10.1139/o11-046.

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A typical eukaryotic genome harbors a rich variety of repetitive elements. The most abundant are retrotransposons, mobile retroelements that utilize reverse transcriptase and an RNA intermediate to relocate to a new location within the cellular genomes. A vast majority of the repetitive mammalian genome content has originated from the retrotransposition of SINE (100–300 bp short interspersed nuclear elements that are derived from the structural 7SL RNA or tRNA), LINE (7kb long interspersed nuclear element), and LTR (2–3 kb long terminal repeats) transposable element superfamilies. Broadly labeled as “evolutionary junkyard” or “fossils”, this enigmatic “dark matter” of the genome possesses many yet to be discovered properties.

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Jeršek, B., P. Gilot, M. Gubina, N. Klun, J. Mehle, E. Tcherneva, N. Rijpens, and L. Herman. "Typing of Listeria monocytogenes Strains by Repetitive Element Sequence-Based PCR." Journal of Clinical Microbiology 37, no. 1 (1999): 103–9. http://dx.doi.org/10.1128/jcm.37.1.103-109.1999.

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Listeria monocytogenes strains possess short repetitive extragenic palindromic (REP) elements and enterobacterial repetitive intergenic consensus (ERIC) sequences. We used repetitive element sequence-based PCR (rep-PCR) to evaluate the potential of REP and ERIC elements for typing L. monocytogenes strains isolated from humans, animals, and foods. On the basis of rep-PCR fingerprints, L. monocytogenes strains were divided into four major clusters matching origin of isolation. rep-PCR fingerprints of human and animal isolates were different from those of food isolates. Computer evaluation of rep-PCR fingerprints allowed discrimination among the tested serotypes 1/2a, 1/2b, 1/2c, 3b, and 4b within each major cluster. The index of discrimination calculated for 52 epidemiologically unrelated isolates of L. monocytogeneswas 0.98 for REP- and ERIC-PCR. Our results suggest that rep-PCR can provide an alternative method for L. monocytogenes typing.

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Dissertations / Theses on the topic "Repetitive element"

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Albarazi, Rayan. "Evaluation of Roadway Embankment Under Repetitive Axial Loading Using Finite Element Analysis." Thesis, Luleå tekniska universitet, Institutionen för samhällsbyggnad och naturresurser, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-81916.

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Razavi, Borghei Seyyed Moein. "The Modeling of Partial Discharge under Fast, Repetitive Voltage Pulses Using Finite-Element Analysis." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/98001.

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By 2030, it is expected that 80% of all electric power will flow through power electronics systems. Wide bandgap power modules that can tolerate higher voltages and currents than silicon-based modules are the most promising solution to reducing the size and weight of power electronics systems. These wide-bandgap power modules constitute powerful building blocks for power electronics systems, and wide bandgap-based converter/power electronics building blocks are envisaged to be widely used in power grids in low- and medium-voltage applications and possibly in high-voltage applications for high-voltage direct current and flexible alternating current transmission systems. One of the merits of wide bandgap devices is that their slew rates and switching frequencies are much higher than silicon-based devices. However, from the insulation side, frequency and slew rate are two of the most critical factors of a voltage pulse, influencing the level of degradation of the insulation systems that are exposed to such voltage pulses. The shorter the rise time, the shorter the lifetime. Furthermore, lifetime dramatically decreases with increasing frequency. Thus, although wide bandgap devices are revolutionizing power electronics, electrical insulating systems are not prepared for such a revolution; without addressing insulation issues, the electronic power revolution will fail due to dramatically increased failure rates of electrification components. In this regard, internal partial discharges (PDs) have the most effect on insulation degradation. Internal PDs which occur in air-filled cavities or voids are localized electrical discharges that only partially bridge the insulation between conductors. Voids in solid or gel dielectrics are challenging to eliminate entirely and may result simply during manufacturing process. The objective of this study is to develop a Finite-Element Analysis (FEA) PD model under fast, repetitive voltage pulses, which has been done for the first time. The model is coded and implemented in COMSOL Multiphysics linked with MATLAB, and its simulation results are validated with experimental tests. Using the model, the influence of different parameters including void shape, void size, and void air pressure on PD parameters are studied.
M.S.
To decarbonize and reduce energy consumption for commercial aviation, the development of lightweight and ultra-efficient all-electric powertrain including electric motors, drives, and associated thermal management systems has been targeted. Using wide bandgap (WBG) power modules that can tolerate high voltages and currents can reduce the size and weight of the drive. However, the operation of WBG-based power converter can endanger the reliability of the electrified systems, most importantly, the insulation system. In this study, it is attempted to model the impact of such threats to the insulation system using numerical models.

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Yoshimoto, Hideki. "Pulse and rhythm : exploring the value of repetitive motion as an element of design." Thesis, Royal College of Art, 2015. http://researchonline.rca.ac.uk/1708/.

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With this thesis I want to share my exploration of pulse and rhythm as elements of design. I locate my research on the meeting point of two different contexts: one is the expansion of kinetic art into design projects, resulting in aesthetic use of motion playing wider roles in design, and the other is the expansion, in relation to technological development, of the value of pulse as a design element. My hypothesis is that the value of pulse as an element of design can be heightened by acquiring the aesthetic use of repetitive motion seen in kinetic art, forging emotional communication with viewers/users. The mission of this research is to demonstrate this argument through practice, collecting working ideas and methods. I propose a model of pulse which can be used as a tool to reflect on projects from a new perspective. To forge a workable focus for the research, I articulate a definition of Japanese aesthetics and deploy related criteria of design. My exploration covers three topics - single pulse, pulse synchronisation, and pulse interference. Several ideas and methods were tested across eight projects in total, related to theories from various fields including biology, physiology, psychology, philosophy, mathematics and physics, and inspired by art and design practice. The insights gained from the projects allowed me to expand the scope of the exploration from pulse to rhythm, and I also reflect on my work from this perspective, distinguishing rhythm from pulse. Furthermore, I conducted an interview-based study to look into rhythm inferred from non-pulsing motions, and the insights from the interviews are presented in the thesis with an additional discussion. The output of the research takes two forms: recommendations, as a simpliflied and generalised summary of my findings, and case studies (projects), as a concrete source of inspiration for the reader's own creations. By thus interweaving the practical and theoretical knowledge gained in the research, I believe this work provides a useful contribution to the field of design.

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Bryden, Louis J. "ROn-1 SINES, a short interspersed repetitive element from the genome of oreochromis niloticus and its species distribution in cichlid fishes." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/mq24809.pdf.

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Glugoski, Larissa. "Análise de marcadores cromossômicos em Rineloricaria (Siluriformes: Loricariidae) com ênfase na diversidade cariotípica." UNIVERSIDADE ESTADUAL DE PONTA GROSSA, 2017. http://tede2.uepg.br/jspui/handle/prefix/940.

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Made available in DSpace on 2017-07-21T19:59:47Z (GMT). No. of bitstreams: 1 Larissa Glugoski.pdf: 3355270 bytes, checksum: c1790717a7cb103b4caf05eb10cb56cb (MD5) Previous issue date: 2017-02-23
The Loricariidae family is the largest in the Siluriformes order, being comprised of eight subfamilies. One of these, the Loricariinae subfamily, shows great diversity in respect to the number of chromosomes and karyotype formula, varying in the diploid number (2n) from 36 to 74 chromosomes. This diverse range originated mainly from Robertsonian(Rb) rearrangements. Rineloricaria is the largest genre in the Loricariinae subfamily, its species ranging from 2n = 36 to 70 chromosomes. In spite of this, little is known about which kinds of repetitive DNA gave rise to the events of chromosome fusion or fission. Previous studies have revealed the presence of multiple 5S rDNA sites in specimens of Rineloricaria from the Paraná River Basin, associated to the Robertsonian fission/fusion events. The aim of this work was the molecular characterization of the fragile sites associated to the 5S rDNA, besides localizing in situ marker chromosomes in Rineloricaria latirostris from the Das Pedras River and R. latirostris from the Piumhi River (first described in this work), seeking to understand the 2n diversification in this group. Rineloricaria latirostris from the Pedras River exhibited 2n = 46 chromosomes, while those from the Piumhi River presented 2n = 48 chromosomes, and both had a fundamental number (FN) of 60. Fluorescence in situ hybridization (FISH) assays in R. latirostris from the Piumhi River revealed 2 chromosome pairs with 5S rDNA sites, pair 7 with 18S rDNA, and only terminal staining when subjected to a telomeric probe (TTAGGGn). The population of the Pedras river exhibited 5 pairs with 5S rDNA sites, the metacentric (m) pair 2 marked with 18S rDNA, TTAGGGn markers in the terminal regions of the chromosomes, and the presence of interstitial telomeric sites (ITS) in pairs m 1 and m 3. The latter, in synteny with 5S rDNA, is indicative of Robertsonian fusion events. The isolation, cloning and sequencing of the 5S rDNA revealed clones with high sequence identity to 5S rDNA from other species, in addition to the necessary regions for recognition and transcription by RNA polymerase III. One clone of ~700 bp exhibited a degenerated fragment of hAT transposon in its sequence. It was named degenerated 5S rDNA. The fluorescence in situ hybridization assay highlighted chromosomes with co-localized staining for 5S rDNA/hAT, 5S rDNA/degenerated 5S rDNA, and 5S rDNA/ITS (m 3 pair) in R. latirostris from das Pedras River. In R. latirostris from Piumhi River, there was no detection of degenerated 5S rDNA sites. These results allow us to infer the role of the hAT transposon in the dispersion of 5S rDNA sites in the population, since some studies have indicated a relation between 5S rDNA dispersion and transposons in fish. In conclusion, data obtained by this study indicate a possible association between the hAT and the dispersion of 5S rDNA sites and Robertsonian events in the studied population of R. latirostris. The presence of the 5S rDNA/degenerated 5S rDNA/ITS generates hotspots for chromosomal breakage, contributing to the large karyotype diversity found in Loricariidae.
A família Loricariidae é a mais numerosa dentro da ordem Siluriformes e abrange oito subfamílias. A subfamília Loricarinae apresenta uma grande diversidade no que diz respeito ao número de cromossomos e a fórmula cariotípica, com variação do número diploide (2n) de 36 a 74 cromossomos, sendo os rearranjos Robertsonianos (Rb) considerados os principais mecanismos para explicar esta variação cromossômica. Rineloricaria é o gênero mais numeroso de Loricariinae, com espécies apresentando 2n = 36 - 70 cromossomos. Contudo, pouco ainda se sabe sobre quais os tipos de DNAs repetitivos originaram os eventos de fissão e fusão cromossômica. Estudos anteriores revelaram a presença de sítios múltiplos de rDNA 5S em exemplares de Rineloricaria da bacia do Rio Paraná, associados aos eventos de fissão/fusão Robertsonianos. O objetivo deste trabalho foi a caracterização molecular de sítios frágeis associados ao rDNA 5S, além da localização in situ de marcadores cromossômicos em Rineloricaria latirostris do rio das Pedras e R. latirostris do rio Piumhi (pela primeira vez descrito neste trabalho), visando a compreensão da diversificação do 2n neste grupo. Rineloricaria latirostris do rio das Pedras apresentou 2n = 46 cromossomos, enquanto R. latirostris do rio Piumhi apresentou 2n = 48 cromossomos, ambos com número fundamental (NF) de 60. Ensaios de hibridação in situ fluorescente em R. latirostris do rio Piumhi revelaram 2 pares cromossômicos marcados com rDNA 5S, o par 7 marcado com rDNA 18S, além de apenas marcações terminais utilizando-se a sonda telomérica (TTAGGGn). A população do rio das Pedras apresentou 5 pares portadores de sítios de rDNA 5S, o par metacêntrico (m) 2 marcado com rDNA 18S, marcações de TTAGGGn nas regiões terminais dos cromossomos, além da presença de vestígios de sítios teloméricos intersticiais (interstitial telomeric sites - ITS) nos pares m 1 e m 3, sendo este último em sintenia com o rDNA 5S, indicativo de eventos de fusão Robertsoniana. O isolamento, clonagem e sequenciamento de fragmentos de rDNA 5S, revelaram clones apresentando alta identidade ao rDNA 5S de outras espécies, além das regiões necessárias para o reconhecimento e transcrição pela RNA polimerase III. Um dos clones de ~700 pb apresentou um fragmento do transposon hAT em sua sequência, já em intensa degeneração molecular, sendo denominado de rDNA 5S degenerado. A hibridação in situ fluorescente evidenciou cromossomos com marcações co-localizadas de rDNA 5S/hAT, rDNA 5S/rDNA 5S degenerado e rDNA 5S/ITS (no par m 3) em R. latirostris do rio da Pedras. Em R. latirostris do rio Piumhi, não foram detectados sítios com rDNA 5S degenerado. Estes resultados nos permitem inferir o papel do TE hAT na dispersão dos sítios de rDNA 5S na população estudada, visto que alguns estudos indicam haver uma relação entre a dispersão do rDNA 5S pelo genoma e TEs em peixes. Em conclusão, os dados obtidos neste estudo indicam uma possível associação entre o elemento hAT e a dispersão de sítios de rDNA 5S e eventos Robertsonianos presentes na população de R. latirostris estudada. A presença de rDNA 5S/rDNA 5S degenerado/ITS geram hotspots para as quebras cromossômicas, contribuindo assim para a ampla diversidade cariotípica encontrada em Loricariidae.

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Motta, V. "DIFFERENTIAL SUSCEPTIBILITY OF REPETITIVE ELEMENTS TO AIRBORNE POLLUTANTS." Doctoral thesis, Università degli Studi di Milano, 2013. http://hdl.handle.net/2434/216407.

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Background. Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has been associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. Objective. To evaluate sensitivity of DNA methylation and expression in differentially‐evoluted LINE, Alu, and HERV subfamilies to different types of airborne pollutants. Methods. We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM10) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‐evoluted repetitive element subfamilies. We evaluate sensitivity of DNA methylation of the same 10 subfamilies and the expression of the most representative and well studied subfamilies AluSx and L1HS in a more wide population of 120 individuals (Beijing Truck Driver Air Pollution Study, BTDAS) with a well characterized personal exposure levels of PM2.5 and ambient PM10. Results. In the three studies, high-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study, dose-response analyses showed subfamily-specific correlations of methylation with exposure levels. Interaction models showed that the effects of the exposures on DNA methylation were dependent on the subfamily evolutionary age, with stronger effects on older LINEs from PM10 (p‐interaction=0.003) and benzene (p‐interaction=0.04), and on younger Alus from PM10 (p-interaction=0.02). In the BTDA Study the group analysis showed a significantly lower DNA methylation in the truck drivers group in AluSx (P=0.02) and MLT1d (P=0.01). The dose response analysis confirmed a lower AluSx methylation in relation to PM10 8-day mean (P=0.047) and a lower MLT1d methylation in relation to exposure to PM2.5 (P=0.002), EC (P=0.008), ambient PM10 study day mean (P=0.005) and ambient PM10 8-day mean (P=0.018). Conclusions. The evolutionary age of repetitive element subfamilies determines differential susceptibility of DNA methylation and expression to airborne pollutants.

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Ward, Michelle Claire. "The regulatory potential of repetitive elements in mammalian genomes." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648276.

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Hypský, Jan. "Rekonstrukce repetitivních elementů DNA." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2018. http://www.nusl.cz/ntk/nusl-385940.

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Eukaryotic genomes contain a large number of repetitive structures. Their detection and assembly today are the main challenges of bioinformatics. This work includes a classification of repetitive DNA and represents an implementation of a novel de novo assembler focusing on searching and constructing LTR retrotransposons and satellite DNA. Assembler accepts on his input short reads (single or pair-end), obtained from next-generation sequencing machines (NGS). This assembler is based on Overlap Layout Consensus approach.

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Casas, Masnou Eduard. "A role for heterochromatin and repetitive elements in epigenetic inheritance." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668338.

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Gene regulation mechanisms control the level of transcription of each gene into RNA and the combination of expressed genes determines cell identity. Gene regulation is maintained by epigenetic mechanisms including DNA methylation, histone modifications and non-coding RNAs. These same mechanisms are responsible for silencing of transposable elements and heterochromatin formation. Interestingly, epigenetic mechanisms can transmit the transcriptional state of a gene to the next generation. Epigenetic inheritance differs from conventional genetics: it does not follow the law of segregation and importantly, can transmit acquired traits. The advent of next generation sequencing (NGS) allows for gene expression quantification and epigenome profiling, opening the door to genome wide screenings of epigenetic factors and phenotypes linked to epigenetic inheritance. Here, I study the role of heterochromatin and transposable elements in epigenetic inheritance. In the first chapter I present how an IAP insertion in the Nocturnin gene triggers the birth of new piRNA cluster in mouse. We hypothesize that many piRNA producing loci have evolved from ERV insertions into germline expressed genes. Last, we identify NXF1 as a key factor in piRNA biogenesis of IAP-derived piRNA loci. In the second chapter I test whether the IAP insertion in Nocturnin, and therefore piRNAs produced from this gene in the male germline, affect expression of the gene in the embryo. I find that the piRNA-producing allele of Nocturnin is more highly expressed from the paternal that the maternal allele in early embryo. Thus, the IAP insertion in Nocturnin leads to transmission of an altered epigenetic expression state from parents to progeny, potentially via the production of piRNAs in the male germline. In the third chapter of this thesis I describe a model of intergenerational epigenetic inheritance in flies. My work describes genome wide changes in gene expression that are direct consequences of epigenetic inheritance and I identify chromatin factors related to the transmission and maintenance of the phenotype in the next generation. In the fourth chapter of my thesis I use worms exposed to high temperature to identify endogenous genes that are able to maintain memory of expression for many generations. Interestingly, I find that transposable elements that are upregulated by temperature and repressed by heterochromatin can transmit epigenetic information to the progeny. In the fifth chapter of this thesis I study heritable expression of acquired expression states after epigenetic information loss linked to impaired DNA replication. My work describes how the loss of repressive marks during impaired replication in embryos leads to heritable changes in gene expression of loci regulated by heterochromatin and polycomb means.
Els mecanismes de regulació gènica controlen el nivell de transcripció de cada gen I l’estabilitat dels ARNs produïts. El perfil d’expressió gènica determina la identitat d’una cèl·lula, permetent que es formin teixits diferenciats partint d’exactament el mateix ADN. L’epigenètica és el conjunt de factors que asseguren que es mantingui el patró d’expressió gènica durant les divisions cel·lulars i el temps, i inclouen mecanismes com la metilació de l’ADN i la cromatina. També són responsables del silenciament d’elements repetitius i exògens presents al genoma. En aquesta tesi estudio el rol de l’epigenètica en transmetre informació d’expressió gènica no lligada a la seqüència d’ADN a les següents generacions. En concret, em centro en el paper que juguen l’heterocromatina i els elements repetitius en mantenir i transmetre canvis d’expressió a les següents generacions.

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10

Carter, Andrew T. "VL30 : a mouse retrovirus-like family of repetitive DNA elements." Thesis, University of Warwick, 1985. http://wrap.warwick.ac.uk/67115/.

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Mouse and rat cells encode an abundant 30S RNA which shares many structural properties with retroviral genomic RNA. This VL30 RNA can be efficiently packaged into retrovirus particles. Mouse cells recently infected with a MuLV (VL30) pseudotype were shown to contain full length, reverse-transcribed DNA copies of both RNA species. VL30 DNA could also be synthesized in quantity using the endogenous reverse transcriptase activity of detergent-disrupted MuLV (VL30) particles. This DNA was found to be identical to that produced in vivo. Several 4.6-4.9kbp molecular clones (NVL clones) of VL30 cDNA were obtained. The retrovirus-like LTRs of each clone displayed a moderate restriction enzyme site heterogeneity, but NVL unique sequence was identical in each case. Southern blotting experiments using NVL probes showed that (a) most of the 100-200 NIH-3T3 DNA mouse VL30 elements were organized into provirus-like structures with a high degree of sequence conservation, and (b) the majority of these elements were hypermethylated and transcriptionally inactlve, whereas an expressed NVL-like sub-class could account for no more than 5% of mouse VL30 genes. NVL-related sequences in rodent DNAs other than the mouse were markedly less abundant and showed a greater sequence divergence. This was in contrast to MuLV-related sequences whose copy number and homology to a cloned MuLV probe decreased more gradually with phylogenetic distance from the mouse. Sub-genomic NVL probes showed that two rodent species had each conserved a different block of NVL-like sequence. These data indicate that each family has exhibited a different rate of sequence divergence during rodent evolution. Finally, a MuLV (VL30)-infected rat fibroblast line was shown to have received 1-2 copies per cell of a transcriptionally active NVL-like element. This suggests the possibility that evolution of each rodent VL30 family has been influenced by retrovirus-mediated transmission across the species barrier.

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Books on the topic "Repetitive element"

1

Baller, Lisa Maria. Analysis of a dispersed repetitive DNA element in Sclerotinia sclerotiorum. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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Carter, Andrew T. VL30: A mouse retrovirus-like family of repetitive DNA elements. [s.l]: typescript, 1985.

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Robert, Trivers, ed. Genes in conflict: The biology of selfish genetic elements. Cambridge, Mass: Belknap Press of Harvard University Press, 2006.

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J, Miller Wolfgang, and Capy Pierre, eds. Mobile genetic elements: Protocols and genomic applications. Totowa, N.J: Humana Press, 2004.

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Ferraresi, Gisella. Adverbial connectives. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198813545.003.0006.

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In this chapter, the rise and grammaticalization process of the adverbial connective elements aber and allerdings are discussed. Aber ‘but, however’, one of the oldest connectives, is attested in OHG as a VP adverb with restitutive meaning and as an IP adverb with repetitive meaning. Through a reanalysis, aber has come to be newly defined as an exponent of the category Coordination Phrase (CoorP). However, aber is only syntactically a coordinative element in the very first position. In other positions, it is syntactically an adverbial and semantically a coordinative element. The second adverbial connective considered in this chapter, i.e. allerdings ‘however’, has undergone a similar development from a VP adverb to a sentence adverb and later to a connective element. However, allerdings is syntactically still an adverbial element, also in the first position.

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Chamberlain, John William. Molecular cloning and characterization of HSAG-1, a middle repetitive genetic element capable of determining a cell surface antigen correlated with human chronic lymphocytic leukemia. 1985.

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Tengelsen, Leslie A. Characterization of interferon and retroposon-like repetitive elements in salmonid fish. 1992.

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Miller, Wolfgang J., and Pierre Capy. Mobile Genetic Elements. Humana Press, 2010.

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Mullany, Peter, and Adam P. Roberts. Bacterial Integrative Mobile Genetic Elements. Taylor & Francis Group, 2022.

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Bacterial Integrative Mobile Genetic Elements. Taylor & Francis Group, 2013.

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Book chapters on the topic "Repetitive element"

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Vershinin, Alexander V., Thomas Lux, Heidrun Gundlach, Evgeny A. Elisafenko, Jens Keilwagen, Klaus F. X. Mayer, and Manuel Spannagl. "The Gene and Repetitive Element Landscape of the Rye Genome." In Compendium of Plant Genomes, 117–33. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-83383-1_8.

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Rasmussen, U., and M. M. Svenning. "Genomic Fingerprinting and Diversity Studies on Cyanobacteria by Repetitive Element PCR." In Biological Nitrogen Fixation for the 21st Century, 588. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-5159-7_371.

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Rodriguez-Barradas, M. C. "Characterization of Isolates of Bartonella henselae by Repetitive Element PCR." In Bartonella and Afipia Species Emphasizing Bartonella henselae, 143–53. Basel: KARGER, 1998. http://dx.doi.org/10.1159/000060460.

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Karatağ, Hüseyin, Seyhan Firat, and Nihat Sinan Işik. "Evaluation of Flexible Highway Embankment Under Repetitive Wheel Loading Using Finite Element Analysis." In Lecture Notes in Civil Engineering, 705–16. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-63709-9_54.

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Hiett, Kelli L., and Bruce S. Seal. "Use of Repetitive Element Palindromic PCR (rep-PCR) for the Epidemiologic Discrimination of Foodborne Pathogens." In Methods in Molecular Biology, 49–58. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-999-4_5.

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Wicaksono, Danar, Arif Wibowo, and Ani Widiastuti. "Genetic Diversity of Pyricularia oryzae, the Causal Agent of Rice Blast Disease, Based on Repetitive Element–Based Polymerase Chain Reaction." In Proceeding of the 1st International Conference on Tropical Agriculture, 41–47. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-60363-6_4.

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Jachowicz, Joanna W. "Epigenetic Manipulation of Transposable and Repetitive Elements." In Transposable Elements, 355–68. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2883-6_16.

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Kiefer, Christiane. "Repetitive Elemente und das Pflanzengenom." In Genomevolution bei Pflanzen, 25–28. Wiesbaden: Springer Fachmedien Wiesbaden, 2021. http://dx.doi.org/10.1007/978-3-658-33025-5_4.

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Bao, Lisui, and Zhanjiang Liu. "Analysis of Repetitive Elements in the Genome." In Bioinformatics in Aquaculture, 86–97. Chichester, UK: John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781118782392.ch5.

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Yoshioka, Yasushi, Yoshito Takahashi, Shogo Matsumoto, Shoko Kojima, Ken Matsuoka, Kenzo Nakamura, Kazuhiko Ohshima, Norihiro Okada, and Yasunori Machida. "Mechanisms of T-DNA transfer and integration into plant chromosomes: role of vir B, vir D4 and vir E2 and a short interspersed repetitive element (SINE) from tobacco." In Developments in Plant Pathology, 231–48. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0746-4_17.

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Conference papers on the topic "Repetitive element"

1

Borghei, Moein, and Mona Ghassemi. "Partial Discharge Finite Element Analysis under Fast, Repetitive Voltage Pulses." In 2019 IEEE Electric Ship Technologies Symposium (ESTS). IEEE, 2019. http://dx.doi.org/10.1109/ests.2019.8847797.

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Vlaicu, Dan, and Mike Stojakovic. "Probabilistic Models to Approximate Highly Repetitive Linear and Nonlinear Finite Element Analyses of Nuclear Components." In ASME 2009 Pressure Vessels and Piping Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/pvp2009-77220.

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In the development and technical support of nuclear plants, Engineers have to deal with highly repetitive finite element analyses that involve modeling of local variations of the initial design, local flaws due to corrosion-erosion effects, material properties degradation, and modifications of the loading conditions. This paper presents the development of generic models that emulate the behavior of a complex finite element model in a simplified form, with the statistical representation based on a sampling of base-model data for a variety of test cases. An improved Latin Hypercube algorithm is employed to generate the sampling points based on the number and the range of the variables that are considered in the design space. Four filling methods of the approximation models are discussed in this study: response surface, nonlinear, neural networks, and piecewise polynomial model. Furthermore, a bootstrapping procedure is employed to improve the confidence intervals of the original coefficients, and the single-factor or double-factor analysis of variance is applied to determine whether a significant influence exists between the investigated factors. Two numerical examples highlight the accuracy and efficiency of the methods. The first example is the linear elastic analysis of a pipe bend under pressure loading. The objective of the probabilistic assessment is to determine the relation between the loading conditions as well as the geometrical aspects of this elbow (pipe wall thickness, outside diameter, elbow radius, and maximum ovality tolerance) and the maximum stress in the elbow. The second example is an axisymmetric nozzle under primary and secondary cycling loads. Variations of the geometrical dimensions, nonlinear material properties, and cycling loading are taken as the input parameters, whereas the response variable is defined in terms of Melan’s theorem translated into the Nonlinear Superposition Method.

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3

Nor, Fethma M., Norhakimin Osman, and Denni Kurniawan. "Finite element analysis of repetitive corrugation and straightening die designs for severe plastic deformation of magnesium alloy." In 1ST INTERNATIONAL SEMINAR ON ADVANCES IN METALLURGY AND MATERIALS (i-SENAMM 2019). AIP Publishing, 2020. http://dx.doi.org/10.1063/5.0015825.

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Gil-Romero, Jaime, S. Gregori, M. Tur, and F. J. Fuenmayor. "Dynamic response of periodic infinite structure to arbitrary moving load based on the Finite Element Method." In VI ECCOMAS Young Investigators Conference. València: Editorial Universitat Politècnica de València, 2021. http://dx.doi.org/10.4995/yic2021.2021.12606.

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Dynamics of repetitive structures subjected to moving loads is a common problem in railway engineering. Bridges, rails or catenaries are the most representative periodic structures, on which the train acts as a moving excitation. Usually, these structures are long enough to consider that their dynamic response is in permanent regime. In this work we present a method to obtain the steady-state solution of an infinite periodic structure subjected to a periodic moving load running at constant speed 𝑉𝑉.This problem has been dealt with in the literature by different approaches. Analytical models [1], two-and-a-half dimensional (2.5D) Finite Element models [2] and the Wave Finite Element Method (WFEM) [3] are found to be used. The method proposed in this work is valid for any generic periodic structure because it is modelled by the classical Finite Element Method. It is mathematically simpler and more efficient compared to WFEM, and it avoids the numerical problems that arise when WFEM is applied to catenaries.The proposed method consists of solving the dynamic interaction problem on a single repetitive block of the structure in which the periodicity condition is applied. Each block of length 𝐿𝐿 is excited by the same load. Thus, the periodicity condition states that the solution at the left boundary of the block is the same as at the right boundary but advanced a period 𝑇𝑇=𝐿𝐿/𝑉𝑉. This condition is imposed in the frequency domain and a procedure to shift into the time domain is presented.

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5

Gomez, Stephanie, James I. McDonald, Elisa Arthofer, Noor Diab, Aneil Srivastava, Paul Austin, and Katherine B. Chiappinelli. "Abstract B58: The role of mutant P53 in repetitive element regulation and the immune response in ovarian cancer." In Abstracts: AACR Special Conference on Advances in Ovarian Cancer Research; September 13-16, 2019; Atlanta, GA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3265.ovca19-b58.

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Kypuros, Javier A., and Raul G. Longoria. "Variable Fidelity Modeling of Vehicle Ride Dynamics Using an Element Activity Metric." In ASME 2002 International Mechanical Engineering Congress and Exposition. ASMEDC, 2002. http://dx.doi.org/10.1115/imece2002-39288.

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The evolving ability of vehicle simulation packages continues to facilitate the use of complex models for virtual prototyping. In formulating a virtual proving ground for conducting vehicle mission studies, it can be helpful to devise ways to facilitate the synthesis of models optimized for repetitive study of specific missions or maneuvers. Because subsystem models may have inherently different bandwidth characteristics, complex vehicle simulations that incorporate such models may be numerically stiff. Furthermore, complexity generally makes it difficult to interpret results and identify key parameters that affect dominant dynamics. The intent of this study is to examine the feasibility of optimizing simulation efficiency and/or enhancing physical insight using a variable fidelity approach that switches between reduced sub models optimized for specific dynamic intervals of the mission study. Because of its established use for model reduction, element activity is tested as a metric to measure and vary model fidelity of a vehicle ride mode model.

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7

Xu, H., and K. Komvopoulos. "Fracture Mechanics Analysis of Asperity Cracking Due to Repetitive Sliding Contact." In STLE/ASME 2010 International Joint Tribology Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/ijtc2010-41162.

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Asperity failure due to repetitive sliding is a common process of wear particle formation. Linear elastic fracture mechanics and the finite element method (FEM) were used to analyze asperity cracking due to sliding against another rigid asperity. The maximum ranges of the tensile and shear stress intensity factors (SIFs) were used to determine the crack growth direction and the dominant mode of fracture. Simulations of repetitive sliding showed a strong dependence of the wear particle size and wear rate on the direction and rate of crack growth. The maximum ranges of tensile and shear SIFs were used to determine the dominant mode of crack growth. The effects of asperity interaction depth, sliding friction, initial crack position, crack-face friction, and material properties on crack growth direction, dominant fracture mode, and crack growth rate are discussed in the context of FEM results. It is shown that the asperity interaction depth and sliding friction exhibit the most pronounced effects on the crack growth direction and growth rate. A transition from shear- to tensile-dominant mode of crack growth was observed with the increase of the asperity interaction depth and/or sliding friction coefficient. Crack-face opening, slip, and stick mechanisms are discussed in the light of crack mechanism maps constructed for different asperity interaction depths and sliding friction coefficients.

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8

Pe´rez Arancibia, Ne´stor O., Chi-Ying Lin, Tsu-Chin Tsao, and James S. Gibson. "Adaptive and Repetitive Control for Rejecting Repeatable and Non-Repeatable Runout in Rotating Devices." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-43534.

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This paper presents a control scheme for rejecting both repeatable and non-repeatable runout components of disturbances occurring in rotational devices. To exemplify this method, implementation and experimental results for track following control of a computer hard disk drive (HDD) read/write heads are presented. Aiming for high performance, the control design involves two steps. The first is the design and tuning of a recursive least-squares (RLS) based scheme intended to achieve minimum variance performance. The second step integrates repetitive and adaptive control schemes in a real-time implementation to compensate for variations and changes in the disturbance dynamics. The repetitive part of this controller targets specific periodic disturbances. The adaptive part compensates for broad bandwidth stochastic disturbances. The key element in this design is the formulation of an appropriate optimization problem, solvable recursively by applying recursive adaptive algorithms. Experimental results obtained from the implementation of this method in a commercial HDD demonstrates the effectiveness of this approach.

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9

Aminfar, Omid, and Amir Khajepour. "Torsional Vibration Analysis of Drillstrings in Blasthole Drilling." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-67418.

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Reducing vibrations in well drilling has a significant effect on improving the overall performance of the drilling process. Vibrations may affect the drilling process in different ways, i.e., reducing durability of the drillstring’s elements, reducing the rate of penetration, and deviating the drilling direction. In rotary drilling, which is used to open mine and oil wells, torsional vibration of the drillstring is an important component of the overall system’s vibration that has received less attention in the literature. In this paper, we propose a finite element model for a sample blasthole drillstring used to open mine wells to investigate its torsional vibrations. Boundary conditions and elements’ specifications are applied to this model. In the model, the interaction between the insert and the rock is represented by a set of repetitive impulses according to the insert pattern. The steady-state response of the system to the repetitive impulses is found and natural frequencies, kinetic energy, and potential energy of the drillstring are calculated. The root mean square (RMS) of the total energy can be used as the measure for reducing the torsional vibration of the system. Finally, an optimum combination of inserts on the cone’s rows was found based on minimizing the total vibratory energy of the drillstring. The optimum design can reduce the torsional vibrations of the drillstring and improve the drilling performance.

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10

Zare, Saeid, Hao Wei Lo, Shrabanti Roy, and Omid Askari. "Flame Stability in Inverse Coaxial Injector Using Repetitive Nanosecond Pulsed Plasma." In ASME 2019 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/imece2019-10991.

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Abstract There has been recently a growing interest in the use of methane as a strong candidate for both interplanetary and descent/ascent propulsion solutions. The higher boiling point and higher density of methane compared with hydrogen, makes its storage tank lighter, cheaper and smaller to launch. Methane is abundant in the outer solar system and can be harvested on Mars, Titan, Jupiter, and many other planets and therefore, it can be used in reusable rocket engines. However, there are still some technological challenges in methane engines development path. Among those challenges, ignition reliability and flame stability are of great importance. These challenges can be addressed by integrating low-temperature plasma (LTP) through repetitive nanosecond pulsed (RNP) discharge to the injector design. This research work focuses on Air/CH4 jet flames in a single-element coaxial shear injector coupled with RNP plasma discharge to study the influence of LTP on ignition characteristics and flame stability using advanced diagnostic techniques. The experiments have been performed for different fuel composition, jet velocities, discharge voltages and frequencies at atmospheric conditions. The transient flame behavior including flame oscillation is studied using direct photography by CMOS high-speed camera. The effect of plasma discharge location on flame stability is also investigated. To demonstrate the effectiveness of RNP discharge on liftoff and blowout/blowoff velocities, the jet velocity at the critical conditions is measured in terms of discharge frequencies and the enhancement of flame stability is then evaluated. The collected experimental data have shown that the RNP discharge can significantly extend the flame stability by reducing the liftoff height and increasing the velocity at which blowout/blowoff occurs.

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