Готові списки джерел за темами / Homing sequence

Добірка наукової літератури з теми "Homing sequence"

Автор: Grafiati
Опубліковано: 30 травня 2022
Оновлено: 31 травня 2022

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Статті в журналах з теми "Homing sequence"

1

Takai, Ken, and Koki Horikoshi. "Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool." Applied and Environmental Microbiology 65, no. 12 (December 1, 1999): 5586–89. http://dx.doi.org/10.1128/aem.65.12.5586-5589.1999.

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ABSTRACT Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases.
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2

Bochtler, Matthias. "Indirect DNA Sequence Readout by LAGLIDADG Homing Endonucleases." Structure 24, no. 6 (June 2016): 839–40. http://dx.doi.org/10.1016/j.str.2016.05.008.

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3

Alloatti, Domenico, Giuseppe Giannini, Loredana Vesci, Massimo Castorina, Claudio Pisano, Elena Badaloni, and Walter Cabri. "Camptothecins in tumor homing via an RGD sequence mimetic." Bioorganic & Medicinal Chemistry Letters 22, no. 20 (October 2012): 6509–12. http://dx.doi.org/10.1016/j.bmcl.2012.07.061.

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4

Sibrian-Vazquez, Martha, Xiaoke Hu, Timothy J. Jensen, and M. Graça H. Vicente. "Synthesis and cellular studies of PPIX-homing peptide conjugates." Journal of Porphyrins and Phthalocyanines 16, no. 05n06 (May 2012): 603–15. http://dx.doi.org/10.1142/s1088424612500599.

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Five amphiphilic protoporphyrin IX-peptide conjugates bearing the sequences ATWLPPR, AAhexPQRRSARLSA and cERGDPhe conjugated via the propionic side chains, were synthesized and evaluated in vitro using two cell lines: human carcinoma HEp2 and human leukemia HL-60. All conjugates were found to have low dark- and photo-toxicities in both cell lines, and 3 to 10-fold higher accumulation was observed within HL-60 vs. HEp2 cells, depending on the nature of the peptide sequence. The preferential subcellular sites of localization for all conjugates were found to be the lysosomes in HEp2 cells, and the mitochondria in HL-60 cells, suggesting different mechanisms of cellular internalization.
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5

Birgisdottir, Å. B., and S. D. Johansen. "Reverse splicing of a mobile twin-ribozyme group I intron into the natural small subunit rRNA insertion site." Biochemical Society Transactions 33, no. 3 (June 1, 2005): 482–84. http://dx.doi.org/10.1042/bst0330482.

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A mobile group I intron containing two ribozyme domains and a homing endonuclease gene (twin-ribozyme intron organization) can integrate by reverse splicing into the small subunit rRNA of bacteria and yeast. The integration is sequence-specific and corresponds to the natural insertion site (homing site) of the intron. The reverse splicing is independent of the homing endonuclease gene, but is dependent on the group I splicing ribozyme domain. The observed distribution of group I introns in nature can be explained by horizontal transfer between natural homing sites by reverse splicing and subsequent spread in populations by endonuclease-dependent homing.
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6

Scalley-Kim, Michelle, Audrey McConnell-Smith, and Barry L. Stoddard. "Coevolution of a Homing Endonuclease and Its Host Target Sequence." Journal of Molecular Biology 372, no. 5 (October 2007): 1305–19. http://dx.doi.org/10.1016/j.jmb.2007.07.052.

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7

Tvardovskii, Aleksandr Sergeevich, and Nina Vladimirovna Yevtushenko. "Deriving Homing Sequences for Finite State Machines with Timed Guards." Modeling and Analysis of Information Systems 27, no. 4 (December 20, 2020): 376–95. http://dx.doi.org/10.18255/1818-1015-2020-4-376-395.

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State identification is the well-known problem in the theory of Finite State Machines (FSM) where homing sequences (HS) are used for the identification of a current FSM state, and this fact is widely used in the area of software and hardware testing and verification. For various kinds of FSMs, such as partial, complete, deterministic, non-deterministic, there exist sufficient and necessary conditions for the existence ofpreset and adaptive HS and algorithms for their derivation. Nowadays timed aspects become very important for hardware and software systems and for this reason classical FSMs are extended by clock variables. In this work, we address the problem of checking the existence and derivation of homing sequences for FSMs with timed guards and show that the length estimation for timed homing sequence coincides with that for untimed FSM. The investigation is based on the FSM abstraction of a Timed FSM, i.e. on a classical FSM which describes behavior of corresponding TFSM and inherits some of its properties. When solving state identification problems for timed FSMs, the existing FSM abstraction is properly optimized.
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8

Wuitschick, Jeffrey D., Paul R. Lindstrom, Alison E. Meyer, and Kathleen M. Karrer. "Homing Endonucleases Encoded by Germ Line-Limited Genes in Tetrahymena thermophila Have APETELA2 DNA Binding Domains." Eukaryotic Cell 3, no. 3 (June 2004): 685–94. http://dx.doi.org/10.1128/ec.3.3.685-694.2004.

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ABSTRACT Three insertion elements were previously found in a family of germ line-limited mobile elements, the Tlr elements, in the ciliate Tetrahymena. Each of the insertions contains an open reading frame (ORF). Sequence analysis of the deduced proteins encoded by the elements suggests that they are homing endonucleases. The genes are designated TIE1-1, TIE2-1, and TIE3-1 for Tetrahymena insertion-homing endonuclease. The endonuclease motif occupies the amino terminal half of each TIE protein. The C-terminal regions of the proteins are similar to the APETELA2 DNA binding domain of plant transcription factors. The TIE1 and TIE3 elements belong to families of repeated sequences in the germ line micronuclear genome. Comparison of the genes and the deduced proteins they encode suggests that there are at least two distinct families of homing endonuclease genes, each of which appears to be preferentially associated with a specific region of the Tlr elements. The TIE1 and TIE3 elements and their cognates undergo programmed elimination from the developing somatic macronucleus of Tetrahymena. The possible role of homing endonuclease-like genes in the DNA breakage step in developmentally programmed DNA elimination in Tetrahymena is discussed.
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9

MacGregor, Barbara J., Jennifer F. Biddle, and Andreas Teske. "Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria." Applied and Environmental Microbiology 79, no. 13 (April 19, 2013): 3974–85. http://dx.doi.org/10.1128/aem.03821-12.

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ABSTRACTThe draft genome sequence of a single orangeBeggiatoa(“CandidatusMaribeggiatoa”) filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to thefdxNexcision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceaematches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in otherBeggiatoaceaegenomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.
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10

Chen, Z., F. Wen, N. Sun, and H. Zhao. "Directed evolution of homing endonuclease I-SceI with altered sequence specificity." Protein Engineering Design and Selection 22, no. 4 (January 10, 2009): 249–56. http://dx.doi.org/10.1093/protein/gzp001.

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Дисертації з теми "Homing sequence"

1

Eklund, Jennifer Lee. "Design and characterization of homing endonuclease I-PpoI variants with novel DNA sequence specificity /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/10265.

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2

Мирошник, М. А., П. В. Галкін, О. Б. Зайченко, and Р. И. Цехмистро. "Testability Increasing Method by Introducing Hardware Redundancy in the Easy-tested Finite State Machines." Thesis, NURE, MC&FPGA, 2019. https://mcfpga.nure.ua/conf/2019-mcfpga/10-35598-mcfpga-2019-002.

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Testability increasing methods by introducing hardware redundancy into the circuit implementation are sufficiently developed and widely used in the design. Since the construction of the testing sequence is based on the use of automaton diagrams, it eliminates the need to analyze the circuit implementation of the remote control when building a diagnostic experiment. This approach allows us to extend the class of detectable faults, which in structural-analytical test generation methods is limited, as a rule, to a multitude of single constant faults. The use of automaton models in the construction of tests allows to detect any malfunction that changes the automaton diagram of a serviceable remote control and does not increase the number of states of remote control memory elements. There was described finite state machine using hardware description language. The method of computer-aided design of the easytested control FSM by introducing the hardware redundancy is presented in the paper. The FSM model is represented in VHDL in the form of the FSM template. The solution way is to add additional fragments of the VHDL code, which ensure the forced setting of the FSM into an arbitrary state without the use of synchronizing sequences. The use of the shift register in the memory part of the control FSM for organizing the path scanning was considered. The method of FSM state table expansion, which ensures the mode of bypassing all nodes of the FSM’ state diagram in the diagnostic mode was proposed.
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3

Mondal, Mayukh 1989. "New insights into human migration, demography and adaptation of Indian and South Asian populations from genome analyses." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/511362.

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Анотація:
Human genome project published their first human whole genome sequence on 2001 at the cost of billions of dollars. Since, the cost of sequencing is decreasing faster than Moore’s law. Now, we not only have sequenced thousands of modern humans’ whole genome, we also obtained whole genome sequences of extinct hominin and other ancient modern humans with relatively good quality. These sequences granted us some unexpected results: like how recently modern humans left Africa and populated around all over the world (which is called recent African origin model) while doing so how they have admixed with multiple hominin populations. Until now modern biology (unlike physics) always dominated by empirical results compared to theoretical concepts, which forces people to perceive biology as a descriptive science. As we are obtaining more and more data every day, it is now time to push our theoretical concepts before empirical results in biology. Here in this thesis, we provided deeper knowledge about ancestry of Indian, Asian and Pacific populations. We were also able to reveal an unknown hominin population existed even before it is sequenced. In addition to these, we demonstrated strong natural selection could change human morphology drastically in a short period.
El projecte del genoma humà va publicar la primera seqüència completa del genoma humà el 2001 amb un cost de milers de millions de dòlars. Després d'això, el cost de la seqüenciació està disminuint més ràpid que la llei de Moore. Actualment no només tenim la seqüència de del genoma humà, sinó que tenim la de molts humans i d’homínids extingits amb una qualitat relativement bona. L’estudi de les seqüències de molts genomes humans varen proporcionar la base per postular que els humans moderns es varen originar a Àfrica, i en la sortida d’Àfrica (Out Of Africa) varen poblar la resta del món, amb una certa barreja amb diferents poblacions d'homínids. La base del treball en biologia i en genòmica evolutiva ha estat fonamentalment empírica (a diferència de la física), però actualment la disponibilitat de moltes dades permet empenyer la recerca cap a aspectes molt més analítics: aquest és l’enfocament del nostre treball en seqüències de DNA. Aquí, en aquesta tesi, hem proporcionat un coneixement més profund sobre l’origen i l'ascendència de poblacions indígenes, d’Àsia i del Pacífic, centrant-nos en la India continental i especialment en les Illes Andaman. També hem estat capaços de revelar l’existència d’una població d'homínids desconeguts que es va barrejar amb els ancestres d’aquestes poblacions. A més, hem demostrat que una forta selecció natural pot canviar dràsticament la morfologia humana en un curt període de temps i que explicaria la morfologia pigmea del pobladors de les illes Andaman.
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4

Carneiro, Joyce Silva. "Towards Control of Dutch Elm Disease: dsRNAs and the Regulation of Gene Expression in Ophiostoma novo-ulmi." Thesis, 2013. http://hdl.handle.net/1828/4715.

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Ophiostoma novo-ulmi is the causal agent of Dutch elm disease (DED) which has had a severe impact on the urban landscape in Canada. This research program focused on developing molecular genetic strategies to control this pathogenic fungus. The first strategy involved the development of RNA interference (RNAi) for the down-regulation of genes involved in pathogenicity. An efficient RNAi cassette was developed to suppress the expression of the endopolygalacturonase (epg1) locus which encodes a cell-wall degrading enzyme. This epg1-RNAi cassette significantly reduced the amount of polygalacturonase activity in the fungus and resulted in almost complete degradation of epg1 mRNA. The need for a native promoter to selectively down-regulate specific gene loci was addressed by developing a carbon-catabolite regulated promoter (alcA) to drive the expression of the epg1-RNAi cassette. The expression of an alcA-driven epg1-RNAi cassette resulted in the down-regulation of epg expression under glucose starvation but normal levels of expression in high glucose. The expression could therefore be controlled by culture conditions. The second strategy explored the potential of using dsRNA viruses to vector disruptive RNAi cassettes. An isolate of O. novo-ulmi strain 93-1224 collected in the city of Winnipeg, was infected by two dsRNA mitoviruses which upon sequence characterization were named OnuMV1c and OnuMV7. To assess the transmissibility of this dsRNA virus the infected isolate 93-1224 was paired with three naive isolates of the related fungi O. ulmi and O. himal-ulmi. Through the use of nuclear and mitochondrial markers it was determined that the virus OnuMV1c may not rely on mitochondrial fusion for transmission but may have a cytoplasmic transmission route. This investigation of gene expression and manipulation has provided tools to help understand gene regulation in O. novo-ulmi. It has also added to our knowledge of mitoviruses, their transmission and potential use as a biological control. By enhancing our understanding of transmissible hypovirulence this work contributes to efforts to develop a new approach to target DED as well as a potential model for the control of other fungal diseases.
Graduate
0307
0306
0369
jscarneiro@hotmail.com
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Частини книг з теми "Homing sequence"

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Wang, Hung-En, Kuan-Hua Tu, Jie-Hong R. Jiang, and Natalia Kushik. "Homing Sequence Derivation with Quantified Boolean Satisfiability." In Testing Software and Systems, 230–42. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-67549-7_14.

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Ravikumar, B., and X. Xiong. "Implementing sequential and parallel programs for the homing sequence problem." In Lecture Notes in Computer Science, 120–31. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/3-540-63174-7_10.

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Sandberg, Sven. "1 Homing and Synchronizing Sequences." In Model-Based Testing of Reactive Systems, 5–33. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11498490_2.

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Rivest, Ronald L., and Robert E. Schapire. "Inference of finite automata using homing sequences." In Machine Learning: From Theory to Applications, 51–73. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/3-540-56483-7_22.

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Kushik, Natalia, and Nina Yevtushenko. "On the Length of Homing Sequences for Nondeterministic Finite State Machines." In Implementation and Application of Automata, 220–31. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-39274-0_20.

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Kushik, Natalia, and Nina Yevtushenko. "Describing Homing and Distinguishing Sequences for Nondeterministic Finite State Machines via Synchronizing Automata." In Implementation and Application of Automata, 188–98. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-22360-5_16.

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Kushik, Natalia, and Hüsnü Yenigün. "Heuristics for Deriving Adaptive Homing and Distinguishing Sequences for Nondeterministic Finite State Machines." In Testing Software and Systems, 243–48. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-25945-1_15.

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8

Yevtushenko, Nina, Victor Kuliamin, and Natalia Kushik. "Evaluating the Complexity of Deriving Adaptive Homing, Synchronizing and Distinguishing Sequences for Nondeterministic FSMs." In Testing Software and Systems, 86–103. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-31280-0_6.

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9

Kimbel, William H., Yoel Rak, Donald C. Johanson, Ralph L. Holloway, and Michael S. Yuan. "Background." In The Skull of Australopithecus afarensis. Oxford University Press, 2004. http://dx.doi.org/10.1093/oso/9780195157062.003.0004.

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Australopithecus afarensis is a fossil hominin species known from at least four East African Rift Valley sites ranging from northern Ethiopia in the north to northern Tanzania in the south and bridging the time period between approximately 3.6 and 3.0 million years ago (Ma). First identified in the late 1970s as the bipedal but craniodentally apelike rootstock from which later Australopithecus and Homo evolved (Johanson et al., 1978; Johanson and White, 1979), A. afarensis constituted the first substantial record of unequivocal human ancestors older than 3.0 million years (Myr). An array of more recently made discoveries have placed A. afarensis in a pivotal position in early hominin phylogeny, bracketed in time between, on the one hand, two temporally successive species, A. anamensis and Ardipithecus ramidus, that jointly extend the hominin record back to 4.4 Ma (M. Leakey et al., 1995, 1998; White et al., 1994, 1995), and, on the other hand, the earliest strong (stratigraphic) evidence for hominin lineage diversification, with the first known records of A. africanus (ca. 2.7 Ma) in southern Africa, and of A. aethiopicus (ca. 2.7 Ma) and A. garhi (2.5 Ma) in eastern Africa (Walker et al., 1986; Asfaw et al., 1999).2 The task of sorting out the relationships among all of these species hinges on the interpretation of A. afarensis itself, from its alpha taxonomy and phylogenetic role to its pattern of evolution over time. A prerequisite to achieving this goal is a more complete knowledge of the A. afarensis fossil record, narrowing gaps in our knowledge of anatomy and variation, as well as of distributions in space and time. On sample size alone, A. afarensis is the best-known hominin species in the eastern African fossil record. The vast majority of fossils in the A. afarensis hypodigm, some 360 specimens, or approximately 90% of the total, have been recovered at the Hadar site, from the 200+ meter sequence of silts, sands, and clays that comprise the Hadar Formation, which is exposed along the drainages of the Awash River in the Afar Depression of northern Ethiopia (Johanson et al., 1982a; Kimbel et al., 1994).
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Davidson, Iain. "Evolution of Cognitive Archaeology through Evolving Cognitive Systems." In Squeezing Minds From Stones, 79–101. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780190854614.003.0005.

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Tom Wynn’s original work that looked at the evolution of stone tool technology using Piaget’s developmental sequence was the beginning of productive research into the evolution of hominin and human cognition. In this chapter, I evaluate those beginnings and discusses recent attempts to provide a more satisfactory understanding of changes in stone tool technologies, including work by Philip Barnard and William McGrew, subsequent work by Tom Wynn, and my own work with various collaborators. It suggests that some of the previous understandings of cognitive evolution were shaped by the fact that approaches to stone tools were largely determined in the nineteenth century. I propose some new ways of looking at stone tools and the sort of story that allows for more productive models of the evolution of human cognition.
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Тези доповідей конференцій з теми "Homing sequence"

1

Vinarskii, Evgenii, and Nina Yevtushenko. "Evaluating Length of a Shortest Adaptive Homing Sequence for Weakly Initialized FSMs." In 2020 IEEE East-West Design & Test Symposium (EWDTS). IEEE, 2020. http://dx.doi.org/10.1109/ewdts50664.2020.9225043.

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Rivest, R. L., and R. E. Schapire. "Inference of finite automata using homing sequences." In the twenty-first annual ACM symposium. New York, New York, USA: ACM Press, 1989. http://dx.doi.org/10.1145/73007.73047.

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Çirişci, Berk, M. Emek, Ege Sorguç, Kamer Kaya, and Husnu Yenigun. "Using Synchronizing Heuristics to Construct Homing Sequences." In 7th International Conference on Model-Driven Engineering and Software Development. SCITEPRESS - Science and Technology Publications, 2019. http://dx.doi.org/10.5220/0007403503620369.

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Çirişci, Berk, M. Emek, Ege Sorguç, Kamer Kaya, and Husnu Yenigun. "Using Synchronizing Heuristics to Construct Homing Sequences." In 7th International Conference on Model-Driven Engineering and Software Development. SCITEPRESS - Science and Technology Publications, 2019. http://dx.doi.org/10.5220/0007403503640371.

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Vinarskii, Evgenii, Aleksandr Tvardovskii, Larisa Evtushenko, and Nina Yevtushenko. "Deriving adaptive homing sequences for weakly initialized nondeterministic FSMs." In 2019 IEEE East-West Design & Test Symposium (EWDTS). IEEE, 2019. http://dx.doi.org/10.1109/ewdts.2019.8884403.

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Vinarskii, Evgenii, Aleksandr Tvardovskii, and Nina Yevtushenko. "Adaptive Homing Sequences for Partial Weakly-initialized Observable FSMs." In 2021 IEEE East-West Design & Test Symposium (EWDTS). IEEE, 2021. http://dx.doi.org/10.1109/ewdts52692.2021.9581010.

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Deshmukh, R. G., and G. N. Hawat. "An algorithm to determine shortest length distinguishing, homing, and synchronizing sequences for sequential machines." In Proceedings of SOUTHCON '94. IEEE, 1994. http://dx.doi.org/10.1109/southc.1994.498154.

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Lukac, M., M. Kameyama, M. Perkowski, and P. Kerntopf. "Analysis of Reversible and Quantum Finite State Machines Using Homing, Synchronizing and Distinguishing Input Sequences." In 2013 IEEE 43rd International Symposium on Multiple-Valued Logic (ISMVL 2013). IEEE, 2013. http://dx.doi.org/10.1109/ismvl.2013.15.

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Qiao, Na-na, Qiang Gao, Qin Zhao, De-pei Wang, Wen-yi Zhao, and Chang-yan Yu. "The Cloning and Analysis of a Partial Lipase Gene Sequence of Staphylococcus hominis GIMT1.079: Partial Lipase Gene Sequencing of S. hominis." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2010). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5518078.

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Fox, Mathew L. "HOMININ PALEOENVIRONMENTS AND EAST ASIAN MONSOONAL VARIABILITY IN THE QINLING MOUNTAIN REGION OF CENTRAL CHINA: EXAMINING THE ORGANIC GEOCHEMSITRY AND GRAIN SIZE DISTRIBUTIONS OF MID-PLEISTOCENE PALEOLITHIC LOESS-PALEOSOL SEQUENCES." In GSA Annual Meeting in Seattle, Washington, USA - 2017. Geological Society of America, 2017. http://dx.doi.org/10.1130/abs/2017am-305702.

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Звіти організацій з теми "Homing sequence"

1

Millan, Jose L. Sequence Motifs Specifying Homing and Metastasis to Bone. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada407485.

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