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Journal articles on the topic 'Motif significance analysis'
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1
Ng, P., and U. Keich. "GIMSAN: a Gibbs motif finder with significance analysis." Bioinformatics 24, no. 19 (2008): 2256–57. http://dx.doi.org/10.1093/bioinformatics/btn408.
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Zhong, Xuehua, Neocles Leontis, Shuiming Qian, et al. "Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal Its Essential Role in Replication." Journal of Virology 80, no. 17 (2006): 8566–81. http://dx.doi.org/10.1128/jvi.00837-06.
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ABSTRACT RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented in which core non-Watson-Crick base pairs are precisely specified. Isostericity matrix analysis of these base pairs showed that the model accounts for the reported natural sequence variations and viable experimental mutations in loop E motifs of PSTVd and other viroids. Furthermore, isostericity matrix analysis allowed us to design disruptive, as well as compensatory, mutations of PSTVd loop E. Functional analyses of such mutants by in vitro and in vivo experiments demonstrated that loop E structural integrity is crucial for replication, specifically during transcription. Our results suggest that the PSTVd loop E motif exists and functions in vivo and provide loss-of-function genetic evidence for the essential role of a viroid RNA three-dimensional motif in rolling-circle replication. The use of isostericity matrix analysis of non-Watson-Crick base pairing to rationalize mutagenesis of tertiary motifs and systematic in vitro and in vivo functional assays of mutants offers a novel, comprehensive approach to elucidate the tertiary-structure-function relationships for RNA motifs of general biological significance.
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Kulyyassov, Arman, and Ruslan Kalendar. "In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species." Data 5, no. 4 (2020): 111. http://dx.doi.org/10.3390/data5040111.
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High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume of which is increasing every year. Therefore, the development of methods that allow the rapid search and analysis of DNA sequences is urgent. Here, we present a novel motif-based high-throughput sequence scoring method that generates genome information. We found and identified Utf1-like, Fgf4-like, and Hoxb1-like motifs, which are cis-regulatory elements for the pluripotency transcription factors Sox2 and Oct4 within the genomes of different eukaryotic organisms. The genome-wide analysis of these motifs was performed to understand the impact of their diversification on mammalian genome evolution. Utf1-like, Fgf4-like, and Hoxb1-like motif diversity was evaluated across genomes from multiple species.
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Xie, Wen-Jie, Rui-Qi Han, and Wei-Xing Zhou. "Time series classification based on triadic time series motifs." International Journal of Modern Physics B 33, no. 21 (2019): 1950237. http://dx.doi.org/10.1142/s0217979219502370.
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It is of great significance to identify the characteristics of time series to quantify their similarity and classify different classes of time series. We define six types of triadic time-series motifs and investigate the motif occurrence profiles extracted from the time series. Based on triadic time series motif profiles, we further propose to estimate the similarity coefficients between different time series and classify these time series with high accuracy. We validate the method with time series generated from nonlinear dynamic systems (logistic map, chaotic logistic map, chaotic Henon map, chaotic Ikeda map, hyperchaotic generalized Henon map and hyperchaotic folded-tower map) and retrieved from the UCR Time Series Classification Archive. Our analysis shows that the proposed triadic time series motif analysis performs better than the classic dynamic time wrapping method in classifying time series for certain datasets investigated in this work.
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Bernstein, Kara A., Sander Granneman, Alicia V. Lee, Swarnameenakshi Manickam, and Susan J. Baserga. "Comprehensive Mutational Analysis of Yeast DEXD/H Box RNA Helicases Involved in Large Ribosomal Subunit Biogenesis." Molecular and Cellular Biology 26, no. 4 (2006): 1195–208. http://dx.doi.org/10.1128/mcb.26.4.1195-1208.2006.
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ABSTRACT DEXD/H box putative RNA helicases are required for pre-rRNA processing in Saccharomyces cerevisiae, although their exact roles and substrates are unknown. To characterize the significance of the conserved motifs for helicase function, a series of five mutations were created in each of the eight essential RNA helicases (Has1, Dbp6, Dbp10, Mak5, Mtr4, Drs1, Spb4, and Dbp9) involved in 60S ribosomal subunit biogenesis. Each mutant helicase was screened for the ability to confer dominant negative growth defects and for functional complementation. Different mutations showed different degrees of growth inhibition among the helicases, suggesting that the conserved regions do not function identically in vivo. Mutations in motif I and motif II (the DEXD/H box) often conferred dominant negative growth defects, indicating that these mutations do not interfere with substrate binding. In addition, mutations in the putative unwinding domains (motif III) demonstrated that conserved amino acids are often not essential for function. Northern analysis of steady-state RNA from strains expressing mutant helicases showed that the dominant negative mutations also altered pre-rRNA processing. Coimmunoprecipitation experiments indicated that some RNA helicases associated with each other. In addition, we found that yeasts disrupted in expression of the two nonessential RNA helicases, Dbp3 and Dbp7, grew worse than when either one alone was disrupted.
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Gazit, E. "Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic-glycine motif." Bioinformatics 18, no. 6 (2002): 880–83. http://dx.doi.org/10.1093/bioinformatics/18.6.880.
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Dries, Angelyn. "The Hero-Martyr Myth in United States Catholic Foreign Mission Literature, 1893–1925." Missiology: An International Review 19, no. 3 (1991): 305–14. http://dx.doi.org/10.1177/009182969101900304.
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A contextual analysis of the mission literature of several United States Catholic groups engaged in mission outreach to other countries shows extensive use of a hero-martyr motif. Four elements of this motif are examined for their significance for the missionaries themselves and for the advantage this motif carried to persuade United States Catholics to support efforts toward missions abroad at a time when the country was considered, at least by Roman authorities, to be “mission territory.”
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Pillon, Monica C., Kevin H. Goslen, Jacob Gordon, Melissa L. Wells, Jason G. Williams, and Robin E. Stanley. "It takes two (Las1 HEPN endoribonuclease domains) to cut RNA correctly." Journal of Biological Chemistry 295, no. 18 (2020): 5857–70. http://dx.doi.org/10.1074/jbc.ra119.011193.
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The ribosome biogenesis factor Las1 is an essential endoribonuclease that is well-conserved across eukaryotes and a newly established member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain-containing nuclease family. HEPN nucleases participate in diverse RNA cleavage pathways and share a short HEPN nuclease motif (RφXXXH) important for RNA cleavage. Most HEPN nucleases participate in stress-activated RNA cleavage pathways; Las1 plays a fundamental role in processing pre-rRNA. Underscoring the significance of Las1 function in the cell, mutations in the human LAS1L (LAS1-like) gene have been associated with neurological dysfunction. Two juxtaposed HEPN nuclease motifs create Las1's composite nuclease active site, but the roles of the individual HEPN motif residues are poorly defined. Here using a combination of in vivo experiments in Saccharomyces cerevisiae and in vitro assays, we show that both HEPN nuclease motifs are required for Las1 nuclease activity and fidelity. Through in-depth sequence analysis and systematic mutagenesis, we determined the consensus HEPN motif in the Las1 subfamily and uncovered its canonical and specialized elements. Using reconstituted Las1 HEPN-HEPN′ chimeras, we defined the molecular requirements for RNA cleavage. Intriguingly, both copies of the Las1 HEPN motif were important for nuclease function, revealing that both HEPN motifs participate in coordinating the RNA within the Las1 active site. We also established that conformational flexibility of the two HEPN domains is important for proper nuclease function. The results of our work reveal critical information about how dual HEPN domains come together to drive Las1-mediated RNA cleavage.
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Friend, Lindzy D., Dulari D. Shah, Christine Deppong, et al. "A dose-dependent requirement for the proline motif of CD28 in cellular and humoral immunity revealed by a targeted knockin mutant." Journal of Experimental Medicine 203, no. 9 (2006): 2121–33. http://dx.doi.org/10.1084/jem.20052230.
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Activation of naive T cells requires the integration of signals through the antigen receptor and CD28. Although there is agreement on the importance of CD28, there remains controversy on the mechanism by which CD28 regulates T cell function. We have generated a gene-targeted knockin mouse expressing a mutation in the C-terminal proline-rich region of the cytoplasmic tail of CD28. Our analysis conclusively showed that this motif is essential for CD28-dependent regulation of interleukin 2 secretion and proliferation. In vivo analysis revealed that mutation of this motif-dissociated CD28-dependent regulation of cellular and humoral responses in an allergic airway inflammation model. Furthermore, we find an important gene dosage effect on the phenotype of the mutation and provide a mechanistic explanation for the conflicting data on the significance of this motif in CD28 function.
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Ng, P., N. Nagarajan, N. Jones, and U. Keich. "Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone." Bioinformatics 22, no. 14 (2006): e393-e401. http://dx.doi.org/10.1093/bioinformatics/btl245.
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Sadah, Khozinatus, Mazaya Muftiya Al Farabi, and Agus Sunandar. "ANALISIS POTENSI RAGAM HIAS KOMPLEKS MAKAM SUNAN DRAJAT SEBAGAI IDENTITAS BATIK LAMONGAN." GESTALT 2, no. 1 (2020): 75–86. http://dx.doi.org/10.33005/gestalt.v2i1.53.
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ABSTRAKSunan Drajat merupakan salah satu wisata religi potensial di kota Lamongan dengan total pengunjung mencapai 515 ribu di tahun 2017. Selain itu, hal menarik lainnya adalah adanya ragam hias yang menghiasi kompleks makam yang diperkirakan telah ada pada zaman XVI Masehi. Hadirnya ragam hias di kompleks makam dapat dijadikan sumber inspirasi dalam menciptakan motif batik khas Lamongan. Mengingat sumber inspirasi pembuatan batik Lamongan selama ini masih terbatas pada hasil SDA laut, dan hasil bumi, sedangkan pada objek wisata religi tradisi belum terjamah. Oleh karena itu, diperlukan analisis potensi ragam hias kompleks makam Sunan Drajat sebagai bahan inspirasi pembuatan motif batik khas Lamongan. Metode yang digunakan adalah analisis transformasi tradisi AUTOMIC (artefact, technique, utility, material, icon, concept, shape). Adapun tahap-tahapan penyusunan antara lain menentukan transformasi tradisi berupa ragam hias ke dalam modernitas sesuai metode AUTOMIC, menggali makna filosofi ragam hias sebagai soul dari batik, menentukan ornamen utama, pengisi, dan isen sesuai bentuk panel ragam hias, kemudian ornamen tersebut di desain menjadi motif batik. Hasil yang di dapat adalah motif batik yang terinspirasi dari ragam hias kompleks makam memiliki nilai estetis tradisi dan mengandung makna filosofi dari ajaran Sunan Drajat. Manfaat penelitian ini adalah sebagai bahan inspirasi motif batik khas Lamongan berdasarkan ragam hias kompleks makam Sunan Drajat. Kata kunci: ragam hias, Sunan Drajat, batik, LamonganABSTRACTSunan Drajat is one of the potential religious tourism in Lamongan city with a total of 515 thousand visitors in 2017. In addition, another interesting thing is the variety of decoration that adorns the tomb complex which is thought to have existed in the XVI AD. The presence of decoration in the tomb complex can be used as a source of inspiration in creating batik motifs typical of Lamongan. Considering the source of inspiration for making Lamongan batik so far is still limited to the results of the natural resources of the sea, and the results of the earth, while the traditional religious tourism object is not touched. Therefore, it is necessary to analyze the potential of the decorative diversity of the tomb complex of Sunan Drajat as an inspiration for making batik motifs typical of Lamongan. The method used is the analysis of the AUTOMIC tradition transformation (artefact, technique, utility, material, icon, concept, shape). The stages of the arrangement include determining the transformation of tradition in the form of decoration into modernity according to the AUTOMIC method, exploring the philosophical meaning of ornamental diversity as the soul of batik, determining the main ornaments, fillers, and isen according to decorative panel shapes, then the ornaments are designed to be batik motif. The results obtained are batik motifs inspired by the complex decoration of tomb complexes that have aesthetic values and contain philosophical significance from the teachings of Sunan Drajat. The benefit of this research is that it is an inspiration for Lamongan batik motifs based on the decorative complex of Sunan Drajat tomb complex
 ornamental variety, Sunan Drajat, batik, LamonganABSTRAKSunan Drajat merupakan salah satu wisata religi potensial di kota Lamongan dengan total pengunjung mencapai 515 ribu di tahun 2017. Selain itu, hal menarik lainnya adalah adanya ragam hias yang menghiasi kompleks makam yang diperkirakan telah ada pada zaman XVI Masehi. Hadirnya ragam hias di kompleks makam dapat dijadikan sumber inspirasi dalam menciptakan motif batik khas Lamongan. Mengingat sumber inspirasi pembuatan batik Lamongan selama ini masih terbatas pada hasil SDA laut, dan hasil bumi, sedangkan pada objek wisata religi tradisi belum terjamah. Oleh karena itu, diperlukan analisis potensi ragam hias kompleks makam Sunan Drajat sebagai bahan inspirasi pembuatan motif batik khas Lamongan. Metode yang digunakan adalah analisis transformasi tradisi AUTOMIC (artefact, technique, utility, material, icon, concept, shape). Adapun tahap-tahapan penyusunan antara lain menentukan transformasi tradisi berupa ragam hias ke dalam modernitas sesuai metode AUTOMIC, menggali makna filosofi ragam hias sebagai soul dari batik, menentukan ornamen utama, pengisi, dan isen sesuai bentuk panel ragam hias, kemudian ornamen tersebut di desain menjadi motif batik. Hasil yang di dapat adalah motif batik yang terinspirasi dari ragam hias kompleks makam memiliki nilai estetis tradisi dan mengandung makna filosofi dari ajaran Sunan Drajat. Manfaat penelitian ini adalah sebagai bahan inspirasi motif batik khas Lamongan berdasarkan ragam hias kompleks makam Sunan Drajat. Kata kunci: ragam hias, Sunan Drajat, batik, LamonganABSTRACTSunan Drajat is one of the potential religious tourism in Lamongan city with a total of 515 thousand visitors in 2017. In addition, another interesting thing is the variety of decoration that adorns the tomb complex which is thought to have existed in the XVI AD. The presence of decoration in the tomb complex can be used as a source of inspiration in creating batik motifs typical of Lamongan. Considering the source of inspiration for making Lamongan batik so far is still limited to the results of the natural resources of the sea, and the results of the earth, while the traditional religious tourism object is not touched. Therefore, it is necessary to analyze the potential of the decorative diversity of the tomb complex of Sunan Drajat as an inspiration for making batik motifs typical of Lamongan. The method used is the analysis of the AUTOMIC tradition transformation (artefact, technique, utility, material, icon, concept, shape). The stages of the arrangement include determining the transformation of tradition in the form of decoration into modernity according to the AUTOMIC method, exploring the philosophical meaning of ornamental diversity as the soul of batik, determining the main ornaments, fillers, and isen according to decorative panel shapes, then the ornaments are designed to be batik motif. The results obtained are batik motifs inspired by the complex decoration of tomb complexes that have aesthetic values and contain philosophical significance from the teachings of Sunan Drajat. The benefit of this research is that it is an inspiration for Lamongan batik motifs based on the decorative complex of Sunan Drajat tomb complex.Keywords: ornamental variety, Sunan Drajat, batik, Lamongan
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Hao, Jiajing. "Analysis on the Design Style of William Morris Pattern." BCP Social Sciences & Humanities 19 (August 30, 2022): 137–41. http://dx.doi.org/10.54691/bcpssh.v19i.1595.
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William Morris (1834-1896) was a famous artist and designer in Europe in the 19th century, the founder of the Arts and Crafts movement and the father of modern design, with a pivotal position in the design world. The patterns he designed take animals and plants in nature as elements and integrate them into his own pattern design. Through regular arrangement, he created vivid and elegant patterns, which influenced designers from generation to generation. William Morris is of epoch-making significance. This paper analyses the background of the formation of Morris pattern, Morris pattern with plant as motif, color analysis, structural framework and organizational form of Morris pattern.
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Yerzhanova, S. B., and K. K. Baidetova. "PSYCHOLOGICAL AND PHILOLOGICAL ASPECTS OF THE ARCHETYPE." BULLETIN Series Psychology 64, no. 3 (2020): 85–89. http://dx.doi.org/10.51889/2020-3.1728-7847.15.
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In our article, we paid attention to the history of the concept of archetype, studied and analyzed the concepts of archetypal plot, motive, and stopped at its place in literature, mythology, psychology, and culture. We paid special attention to the work of the Swiss scientist-psychologist C. G. Jung, who introduced the term archetype into science and studied it in psychological, philosophical, and cultural aspects. Having identified the first archetypal images shown by Jung, we made an analysis, giving importance to the role of the concept of" collective unconscious " in the archetype. In addition, we determined the scientific significance of philological research. The concepts of archetypal plot and archetypal motif introduced by the Russian scientist Meletensky were defined, and examples of archetypal motifs and plots in mythology were given. We have analyzed the concepts of myth and archetype, citing the scientific justifications in the literature. The development of the mythical motif in the works of modern Kazakh writers requires a detailed study of the concept of archetype. At all times, literature cannot separate itself from its original source –myth. Since the Archetype is closely related to mythology, we believe that the importance of this topic is very high today
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Angerer, Heike. "The superfamily of mitochondrial Complex1_LYR motif-containing (LYRM) proteins." Biochemical Society Transactions 41, no. 5 (2013): 1335–41. http://dx.doi.org/10.1042/bst20130116.
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Mitochondrial LYRM (leucine/tyrosine/arginine motif) proteins are members of the Complex1_LYR-like superfamily. Individual LYRM proteins have been identified as accessory subunits or assembly factors of mitochondrial OXPHOS (oxidative phosphorylation) complexes I, II, III and V respectively, and they play particular roles in the essential Fe–S cluster biogenesis and in acetate metabolism. LYRM proteins have been implicated in mitochondrial dysfunction, e.g. in the context of insulin resistance. However, the functional significance of the common LYRM is still unknown. Analysis of protein–protein interaction screens suggests that LYRM proteins form protein complexes with phylogenetically ancient proteins of bacterial origin. Interestingly, the mitochondrial FAS (fatty acid synthesis) type II acyl-carrier protein ACPM associates with some of the LYRM protein-containing complexes. Eukaryotic LYRM proteins interfere with mitochondrial homoeostasis and might function as adaptor-like ‘accessory factors’.
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Gładkowska, Dorota. "The significance of symbolism and allegory in Cormac McCarthy’s The Road – a new era of post-apocalyptic fiction." Papers in Literature, `10 (July 30, 2022): 171–98. http://dx.doi.org/10.31648/pl.7862.
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McCarthy’s The Road is frequently described as a gloomy dystopia in which the redemption of humanity is impossible. This essay adopts a different perspective and focuses on the impact of the novel’s symbolism on the shifts in its overall message. The analysis leads to uncovering certain oppositions, apparent dichotomies and paradoxes incorporated in the novel’s recurring images and motifs, with particular emphasis on the motif of dream vision. McCarthy’s ascetic style is also considered in terms of its iconicity and functionality. In other words, this essay argues that the symbolically charged elements of The Road, due to their persistence in the text characterised by minimalism, form an intricate pattern which holds the novel’s allegorical message. The point advocated is that McCarthy’s literary symbolism leaves room for redemption in the world presented and signals the possibility of rebirth. It thus has the potential to gradually undermine and eventually subvert the initial perception of the novel as entirely pessimistic. All things considered, The Road is presented as a step forward in the evolution of post-apocalyptic fiction.
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Tong, Xin, Diana Zitserman, Ilya Serebriiskii, Mark Andrake, Roland Dunbrack, and Fabrice Roegiers. "Numb Independently Antagonizes Sanpodo Membrane Targeting and Notch Signaling in Drosophila Sensory Organ Precursor Cells." Molecular Biology of the Cell 21, no. 5 (2010): 802–10. http://dx.doi.org/10.1091/mbc.e09-09-0831.
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In Drosophila , mitotic neural progenitor cells asymmetrically segregate the cell fate determinant Numb in order to block Notch signaling in only one of the two daughter cells. Sanpodo, a membrane protein required for Notch signaling in asymmetrically dividing cells, is sequestered from the plasma membrane to intracellular vesicles in a Numb-dependent way after neural progenitor cell mitosis. However, the significance of Numb-dependent Sanpodo regulation is unclear. In this study, we conducted a structure–function analysis to identify the determinants of Sanpodo targeting in vivo. We identified an NPAF motif in the amino-terminal cytoplasmic tail of Sanpodo, which is conserved among insect Sanpodo homologues. The Sanpodo NPAF motif is predicted to bind directly to the Numb phosphotyrosine-binding domain and is critical for Numb binding in vitro. Deletion or mutation of the NPAF motif results in accumulation of Sanpodo at the plasma membrane in Numb-positive cells in vivo. Genetic analysis of Sanpodo NPAF mutants shows that Numb-dependent Sanpodo endocytic targeting can be uncoupled from Notch signaling regulation. Our findings demonstrate that Sanpodo contains an evolutionarily conserved motif that has been linked to Numb-dependent regulation in vertebrates and further support the model that Numb regulates Notch signaling independently of Sanpodo membrane trafficking in neural progenitor cells.
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Horiguchi, Hirofumi, Hiroya Yurimoto, Toh-Kheng Goh, Tomoyuki Nakagawa, Nobuo Kato, and Yasuyoshi Sakai. "Peroxisomal Catalase in the Methylotrophic Yeast Candida boidinii: Transport Efficiency and Metabolic Significance." Journal of Bacteriology 183, no. 21 (2001): 6372–83. http://dx.doi.org/10.1128/jb.183.21.6372-6383.2001.
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ABSTRACT In this study we cloned CTA1, the gene encoding peroxisomal catalase, from the methylotrophic yeast Candida boidinii and studied targeting of the gene product, Cta1p, into peroxisomes by using green fluorescent protein (GFP) fusion proteins. A strain from which CTA1 was deleted (cta1Δ strain) showed marked growth inhibition when it was grown on the peroxisome-inducing carbon sources methanol, oleate, and d-alanine, indicating that peroxisomal catalase plays an important nonspecific role in peroxisomal metabolism. Cta1p carries a peroxisomal targeting signal type 1 (PTS1) motif, -NKF, in its carboxyl terminus. Using GFP fusion proteins, we found that (i) Cta1p is transported to peroxisomes via its PTS1 motif, -NKF; (ii) peroxisomal localization is necessary for Cta1p to function physiologically; and (iii) Cta1p is bimodally distributed between the cytosol and peroxisomes in methanol-grown cells but is localized exclusively in peroxisomes in oleate- and d-alanine-grown cells. In contrast, the fusion protein GFP-AKL (GFP fused to another typical PTS1 sequence, -AKL), in the context of CbPmp20 andd-amino acid oxidase, was found to localize exclusively in peroxisomes. A yeast two-hybrid system analysis suggested that the low transport efficiency of the -NKF sequence is due to a level of interaction between the -NKF sequence and the PTS1 receptor that is lower than the level of interaction with the AKL sequence. Furthermore, GFP-Cta1pΔnkf coexpressed with Cta1p was successfully localized in peroxisomes, suggesting that the oligomer was formed prior to peroxisome import and that it is not necessary for all four subunits to possess a PTS motif. Since the main physiological function of catalase is degradation of H2O2, suboptimal efficiency of catalase import may confer an evolutionary advantage. We suggest that the PTS1 sequence, which is found in peroxisomal catalases, has evolved in such a way as to give a higher priority for peroxisomal transport to peroxisomal enzymes other than to catalases (e.g., oxidases), which require a higher level of peroxisomal transport efficiency.
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McFadden, Diane C., Bettina C. Fries, Fang Wang, and Arturo Casadevall. "Capsule Structural Heterogeneity and Antigenic Variation in Cryptococcus neoformans." Eukaryotic Cell 6, no. 8 (2007): 1464–73. http://dx.doi.org/10.1128/ec.00162-07.
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ABSTRACT Cryptococcus neoformans is a human pathogenic fungus with a capsule composed primarily of glucuronoxylomannan (GXM) that is important for virulence. Current views of GXM structure postulate a polymer composed of repeating mannose trisaccharide motifs bearing a single β(1,2) glucuronic acid with variable xylose and O-acetyl substitutions to form six triads. GXM from different strains is notoriously variable in triad composition, but it is not known if the polymer consists of one or more motif-repeating units. We investigated the polymeric organization of GXM by using mass spectrometry to determine if its compositional motif arrangement was similar to that of bacterial capsular polysaccharides, namely, a polymer of a single repeating unit. The results were consistent with, and confirmatory for, the current view that the basic unit of GXM is a repeating mannose trisaccharide motif, but we also found evidence for the copolymerization of different GXM repeating units in one polysaccharide molecule. Analysis of GXM from isogenic phenotypic switch variants suggested structural differences caused by glucuronic acid positional effects, which implied flexibility in the synthetic pathway. Our results suggest that cryptococcal capsule synthesis is fundamentally different from that observed in prokaryotes and employs a unique eukaryotic approach, which theoretically could synthesize an infinite number of structural combinations. The biological significance of this capsule construction scheme is that it is likely to confer a powerful avoidance strategy for interactions with the immune system and phagocytic environmental predators. Consistent with this premise, the antigenic variation of a capsular epitope recognized by a nonprotective antibody was observed under different growth conditions.
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Trajković, Jelena. "METATEXTUALITY AND NARRATIVE TECHNIQUES IN STEPHEN SONDHEIM’S INTO THE WOODS ON STAGE AND SCREEN." PHILOLOGIA MEDIANA 14, no. 1 (2022): 456–76. http://dx.doi.org/10.46630/phm.14.2022.32.
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This paper focuses on the transmedial relationship between Stephen Sondheim’s 1987 Broadway musical Into the Woods and its 2014 film adaptation directed by Rob Marshall and produced by Disney Studios. It places emphasis on the various medium-specific narrative devices the two texts employ in order to bring forth the story’s central motif of storytelling. The metatextual motif of storytelling is deconstructed against Stephen Sondheim’s postmodernist ideology as he challenges the closed system within which fairy-tales traditionally figure, drawing attention to the artificiality of the inherited notions of good and evil, and by extension, the fallibility of prescribed narratives. Finally, this paper offers a detailed analysis of narrative layers and narratorial figures in Into the Woods on stage and screen, ultimately concluding that, due to its lack of an omniscient narrative voice to be questioned, the story’s transposition onto the screen fails to reiterate the significance of metatextuality of the central motif that has proven fundamental to Sondheim’s play.
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Taslim, Noriah. "The Religious Connotations of the Sovereign in Destitution in the Malay Hikayat." Malay Literature 27, no. 2 (2014): 229–41. http://dx.doi.org/10.37052/ml.27(2)no2.
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The essay is an attempt to highlight the significance and the extent of religious influence on classical Malay literature. It plans to do this through the analysis of the structural elements of the plot at both at the surface and underlying level. To narrow down the analysis, only one genre of Malay literature, the so-called hikayat romance will be taken as corpus of investigation. To allow room for a more comprehensive analysis within this restricted corpus, two types of hikayat romance will be taken to task; these are the fantasy/court romance and the hagiographical romance. Both of these works are suitable for this study as they exhibit a remarkable level of religious influence in their textual elements. The analysis, however, will focus especially on the “exile motif” which is the controlling and generative element in the plot. Keywords: hikayat romance, generic structure, exile motif, Hindu interpretative model, sufistic interpretative model
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Paternoster, Henry John, Deborah Warr, and Keith Jacobs. "The enigma of the bogan and its significance to class in Australia: A socio-historical analysis." Journal of Sociology 54, no. 3 (2018): 429–45. http://dx.doi.org/10.1177/1440783318769752.
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This analysis offers a historical perspective to chart the contested discourses that inform understandings of the figure of the ‘bogan’, suggesting its evocation reflects unresolved tensions and accumulated meanings left by the various reconfigurations of class politics since colonial settlement in Australia. We focus on three key historical periods to show how socio-political formations influence both classed identities and class relations: the 1890s, when the ethos of the labour movement was established as the central imaginative motif of a nascent Australian nation; the post-war years, when Robert Menzies offered a political project grounded in the experiences of the middle classes; and the 1990s, where there were complex translocations of class allegiances. We trace how several meaning(s) of class have accumulated and been reworked across these periods and, related to this, how the ‘bogan’ is a composite of left- and right-wing political ideas that articulate different kinds of virtue and unworthiness.
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Das, Chinmaya Kumar, Umasankar Nayak, Preetinanda Pati, et al. "Deciphering the Molecular Architecture of a Candidate R-gene (BjuWRR1) Product Mediating White Rust Resistance in Brassica juncea." International Journal of Bio-resource and Stress Management 12, no. 5 (2021): 393–401. http://dx.doi.org/10.23910/1.2021.2205a.
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In this investigation, a three-dimensional model of a R-gene encoded product BjuWRR1 which is known to play a role in white rust resistance in Brassica juncea was developed to synthesize innovative ways for evolving white rust resistant cultivars. The model was built from the amino acid sequence of BjuWRR1 using structural template information of a disease resistance protein (RPP13-like protein 4 of Arabidopsis thaliana) with the help of homology-based modelling approach. Built models were validated for their stereochemical parameters and structural descriptors using Ramachandran plot analysis, protein structure analysis and ERRAT analysis. Structural analysis of BjuWRR1 model revealed that it is composed of three distinct domains namely a coiled-coil domain, a central NB-ARC nucleotide binding domain and a hypervariable leucine-rich repeat domain. Further, canonical conserved motifs such as P-loop, Kinase2-motif and HD-motif were found in the NB-ARC domain. The built model would help in understanding the molecular basis of plant-immunity against white rust pathogen by understanding the significance of inter-domain interactions in BuWRR1 in triggering the activation of downstream defense response against the white rust pathogen by promoting oligomerization of coiled-coil domains through stabilized hydrophobic interactions and interaction with NB-ARC domain. Presence of patches of charged residues in each domain of BjuWRR1 indicated their possible role in intra-molecular interaction with other domains. Therefore, this model can help in designing functional genomic studies to understand the role of intra-molecular interaction in BjuWRR1 to mediate resistance against white rust pathogen.
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Kendall, Sharon L., Philippa Burgess, Ricardo Balhana, et al. "Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2." Microbiology 156, no. 5 (2010): 1362–71. http://dx.doi.org/10.1099/mic.0.034538-0.
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Mycobacterium tuberculosis is able to use a variety of carbon sources in vivo and current knowledge suggests that cholesterol is used as a carbon source during infection. The catabolized cholesterol is used both as an energy source (ATP generation) and as a source of precursor molecules for the synthesis of complex methyl-branched fatty acids. In previous studies, we described a TetR-type transcriptional repressor, kstR, that controls the expression of a number of genes involved in cholesterol catabolism. In this study, we describe a second TetR-type repressor, which we call kstR2. We knocked this gene out in Mycobacterium smegmatis and used microarrays and quantitative RT-PCR to examine the effects on gene expression. We identified a palindromic regulatory motif for KstR2, showed that this motif is present in three promoter regions in mycobacteria and rhodococcus, and demonstrated binding of purified KstR2 to the motif. Using a combination of motif location analysis, gene expression analysis and the examination of gene conservation, we suggest that kstR2 controls the expression of a 15 gene regulon. Like kstR, kstR2 and the kstR2 regulon are highly conserved among the actinomycetes and studies in rhodococcus suggest a role for these genes in cholesterol catabolism. The functional significance of the regulon and implications for the control of cholesterol utilization are discussed.
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Siregar, Siti Asyiah, Sugito Sugito, and Wahyu Tri Atmojo. "HUBUNGAN PENGETAHUAN DAN KEMAMPUAN MENDISAIN ORNAMEN DENGAN HASIL BELAJAR MEMBATIK MOTIF ORNAMEN BATAK ANGKOLA MANDAILING SISWA KELAS X SMK KARYA BUNDA MEDAN." Gorga : Jurnal Seni Rupa 8, no. 2 (2019): 363. http://dx.doi.org/10.24114/gr.v8i2.15267.
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AbstrakPenelitian ini dilakukan di SMK Karya Bunda Medan yang bertujuan untuk membuktikan apakah ada hubungan yang siknifikan antara hubungan pengetahuan ornamen dan kemampuan mendesain ornamen terhadap hasil belajar membatik motif ornamen Batak Angkola Mandailing. Populasi dalam penelitian ini adalah seluruh siswa kelas X SMK Karya Bunda Medan. Pengambilan sampel menggunakan teknik sampel jenuh sebanyak 19 orang dari kelas X. Penelitian ini menggunakan metode korelasional, yaitu penelitian ini mencari ada tidaknya hubungan antara pengetahuan dan kemampuan mendisain ornamen dengan hasil belajar membatik motif ornamen Batak Angkola Mandailing. Teknik Analisis data menggunakan korelasi ganda (R), Uji keberartian dengan formula F. Hasil temuan penelitian: = 0,60, = 0,58 dan = 0,75 menunjukkan bahwa terdapat hubungan pengetahuan dan kemampuan mendisain ornamen dengan hasil belajar membatik motif ornamen Batak Angkola Mandailing, yang dibuktikan dengan Fhitung = 4,87 untuk dk= n-k-1 = 16 a = 0,05 Ftabel = 3,63 ternyata Fhitung >Ftabel (4,87 > 3,63). Besar sumbangan (kontribusi) antara pengetahuan dan kemampuan mendisain ornamen dengan hasil belajar membatik motif ornamen Batak Angkola Mandailing diperoleh r2=62% artinya bahwa X1, dan X2 memberikan kontribusi atau masukan (sumbangan) pada Y rata-rata 62%, sisanya 38% dari variabel lain. Kata Kunci: pengetahuan, mendisain, membatik, angkola, mandailing.AbstractThis research was conducted at SMK Karya Bunda Medan which aims to prove whether there is a significant relationship between the relationship of ornamental knowledge and the ability to design ornaments to the learning outcomes of batik motifs of Angkola Mandailing Batak ornaments. The population in this study were all students of class X SMK Karya Bunda Medan. Sampling using saturated sample technique as many as 19 people from class X. This study uses a correlational method, namely this study looks for whether there is a relationship between knowledge and ability to design ornaments with the results of learning to batik Angkola Mandailing Batak ornament motifs. Data analysis technique uses multiple correlation (R), significance test with formula F. The results of the study: = 0,60, = 0,58 and = 0,75 shows that there is a relationship between knowledge and ability to design ornaments with learning outcomes batik Angkola Batak ornament motifs Mandailing, which is proven by Fcount = 4.87 for dk = nk-1 = 16 a = 0.05 Ftable = 3.63, it turns out Fcount > Ftable (4.87> 3.63). The contribution between knowledge and ability to design ornaments with the results of learning to batik Angkola Mandailing Batak ornament motifs obtained r2 = 62% means X1 and X2 give contribution or input to the learning outcomes of Y averaged 62%, the remaining 38% from other variables. Keywords: knowledge, design, make batik, angkola, mandailing.
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Gottwein, Eva, and Hans-Georg Kräusslich. "Analysis of Human Immunodeficiency Virus Type 1 Gag Ubiquitination." Journal of Virology 79, no. 14 (2005): 9134–44. http://dx.doi.org/10.1128/jvi.79.14.9134-9144.2005.
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ABSTRACT Ubiquitin is important for the release of human immunodeficiency virus type 1 (HIV-1) and several other retroviruses, but the functional significance of Gag ubiquitination is unknown. To address this problem, we decided to analyze Gag ubiquitination in detail. A low percentage of the HIV-1 p6 protein has previously been shown to be ubiquitinated, and published mutagenesis data suggested that Gag ubiquitination is largely lost upon mutation of the two lysine residues in p6. In this study, we show that Gag proteins lacking the p6 domain or the two lysine residues within p6 are ubiquitinated at levels comparable to those of the wild-type Gag protein. We detected monoubiquitinated forms of the matrix (MA), capsid (CA), and nucleocapsid (NC) proteins in mature virus preparations. Protease digestion of Gag polyproteins extracted from immature virions indicated that ubiquitinated MA, CA, and possibly NC are as abundant as ubiquitinated p6. The HIV-1 late-domain motifs PTAP and LRSLF were not required for Gag ubiquitination, and mutation of the PTAP motif even resulted in an increase in the amount of Gag-Ub conjugates detected. Finally, at steady state, ubiquitinated Gag proteins were not enriched in either membrane-associated or virus-derived Gag fractions. In summary, these results indicate that HIV-1 Gag can be monoubiquitinated in all domains and that ubiquitination of lysine residues outside p6 may thus contribute to viral release and/or infectivity.
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You, Guo-Rung, Joseph T. Chang, Hsiao-Fan Li, and Ann-Joy Cheng. "Multifaceted and Intricate Oncogenic Mechanisms of NDRG1 in Head and Neck Cancer Depend on Its C-Terminal 3R-Motif." Cells 11, no. 9 (2022): 1581. http://dx.doi.org/10.3390/cells11091581.
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N-Myc downstream-regulated 1 (NDRG1) has inconsistent oncogenic functions in various cancers. We surveyed and characterized the role of NDRG1 in head and neck cancer (HNC). Cellular methods included spheroid cell formation, clonogenic survival, cell viability, and Matrigel invasion assays. Molecular techniques included transcriptomic profiling, RT-qPCR, immunoblotting, in vitro phosphorylation, immunofluorescent staining, and confocal microscopy. Prognostic significance was assessed by Kaplan–Meier analysis. NDRG1 participated in diverse oncogenic functions in HNC cells, mainly stress response and cell motility. Notably, NDRG1 contributed to spheroid cell growth, radio-chemoresistance, and upregulation of stemness-related markers (CD44 and Twist1). NDRG1 facilitated cell migration and invasion, and was associated with modulation of the extracellular matrix molecules (fibronectin, vimentin). Characterizing the 3R-motif in NDRG1 revealed its mechanism in the differential regulation of the phenotypes. The 3R-motif displayed minimal effect on cancer stemness but was crucial for cell motility. Phosphorylating the motif by GSK3b at serine residues led to its nuclear translocation to promote motility. Clinical analyses supported the oncogenic function of NDRG1, which was overexpressed in HNC and associated with poor prognosis. The data elucidate the multifaceted and intricate mechanisms of NDRG1 in HNC. NDRG1 may be a prognostic indicator or therapeutic target for refractory HNC.
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Ma, L., A. Westbroek, A. G. Jochemsen, et al. "Mutational analysis of ERCC3, which is involved in DNA repair and transcription initiation: identification of domains essential for the DNA repair function." Molecular and Cellular Biology 14, no. 6 (1994): 4126–34. http://dx.doi.org/10.1128/mcb.14.6.4126-4134.1994.
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The human ERCC3 gene, which corrects specifically the nucleotide excision repair defect in human xeroderma pigmentosum group B and cross-complements the repair deficiency in rodent UV-sensitive mutants of group 3, encodes a presumed DNA helicase that is identical to the p89 subunit of the general transcription factor TFIIH/BTF2. To examine the significance of the postulated functional domains in ERCC3, we have introduced mutations in the ERCC3 cDNA by means of site-specific mutagenesis and have determined the repair capacity of each mutant to complement the UV-sensitive phenotype of rodent group 3 cells. A conservative substitution of arginine for the invariant lysine residue in the ATPase motif (helicase domain I), six deletion mutations in the other helicase domains, and a deletion in the potential helix-turn-helix DNA-binding motif fail to complement the ERCC3 excision repair defect of rodent group 3 mutants, which implies that the helicase domains as well as the potential DNA-binding motif are required for the repair function of ERCC3. Analysis of carboxy-terminal deletions suggests that the carboxy-terminal exon may comprise a distinct determinant for the DNA repair function. In addition, we show that a functional epitope-tagged version of ERCC3 accumulates in the nucleus. Deletion of the putative nuclear location signal impairs neither the nuclear location nor the repair function, indicating that other sequences may (also) be involved in translocation of ERCC3 to the nucleus.
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Ma, L., A. Westbroek, A. G. Jochemsen, et al. "Mutational analysis of ERCC3, which is involved in DNA repair and transcription initiation: identification of domains essential for the DNA repair function." Molecular and Cellular Biology 14, no. 6 (1994): 4126–34. http://dx.doi.org/10.1128/mcb.14.6.4126.
Full textAbstract:
The human ERCC3 gene, which corrects specifically the nucleotide excision repair defect in human xeroderma pigmentosum group B and cross-complements the repair deficiency in rodent UV-sensitive mutants of group 3, encodes a presumed DNA helicase that is identical to the p89 subunit of the general transcription factor TFIIH/BTF2. To examine the significance of the postulated functional domains in ERCC3, we have introduced mutations in the ERCC3 cDNA by means of site-specific mutagenesis and have determined the repair capacity of each mutant to complement the UV-sensitive phenotype of rodent group 3 cells. A conservative substitution of arginine for the invariant lysine residue in the ATPase motif (helicase domain I), six deletion mutations in the other helicase domains, and a deletion in the potential helix-turn-helix DNA-binding motif fail to complement the ERCC3 excision repair defect of rodent group 3 mutants, which implies that the helicase domains as well as the potential DNA-binding motif are required for the repair function of ERCC3. Analysis of carboxy-terminal deletions suggests that the carboxy-terminal exon may comprise a distinct determinant for the DNA repair function. In addition, we show that a functional epitope-tagged version of ERCC3 accumulates in the nucleus. Deletion of the putative nuclear location signal impairs neither the nuclear location nor the repair function, indicating that other sequences may (also) be involved in translocation of ERCC3 to the nucleus.
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Madisch, Ijad, Soeren Hofmayer, Christian Moritz, et al. "Phylogenetic Analysis and Structural Predictions of Human Adenovirus Penton Proteins as a Basis for Tissue-Specific Adenovirus Vector Design." Journal of Virology 81, no. 15 (2007): 8270–81. http://dx.doi.org/10.1128/jvi.00048-07.
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ABSTRACT The penton base is a major capsid protein of human adenoviruses (HAdV) which forms the vertices of the capsid and interacts with hexon and fiber protein. Two hypervariable loops of the penton are exposed on the capsid surface. Sequences of these and 300 adjacent amino acid residues of all 51 HAdV and closely related simian adenoviruses were studied. Adjacent sequences and predicted overall secondary structure were conserved. Phylogenetic analysis revealed clustering corresponding to the HAdV species and recombination events in the origin of HAdV prototypes. All HAdV except serotypes 40 and 41 of species F exhibited an integrin binding RGD motif in the second loop. The lengths of the loops (HVR1 and RGD loops) varied significantly between HAdV species with the longest RGD loop observed in species C and the longest HVR1 in species B. Long loops may permit the insertion of motifs that modify tissue tropism. Genetic analysis of HAdV prime strain p17′H30, a neutralization variant of HAdV-D17, indicated the significance of nonhexon neutralization epitopes for HAdV immune escape. Fourteen highly conserved motifs of the penton base were analyzed by site-directed mutagenesis of HAdV-D8 and tested for sustained induction of early cytopathic effects. Thus, three new motifs essential for penton base function were identified additionally to the RGD site, which interacts with a secondary cellular receptor responsible for internalization. Therefore, our penton primary structure data and secondary structure modeling in combination with the recently published fiber knob sequences may permit the rational design of tissue-specific adenoviral vectors.
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Zhang, Wen, Zhengquan Cai, Mingzhu Kong, et al. "Prognostic significance of TRIM28 expression in patients with breast carcinoma." Open Medicine 16, no. 1 (2021): 472–80. http://dx.doi.org/10.1515/med-2021-0263.
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Abstract Background Tripartite motif 28 (TRIM28) plays a role in multiple biological functions. The expression and function of TRIM28 in breast carcinoma (BC) remain unclear. The aim of this study was to explore potential association of TRIM28 with tumor features and survival. Materials and methods Specimens were collected from BC and adjacent normal tissues. Quantitative reverse transcription PCR (RT-qPCR) and immunohistochemistry (IHC) were performed to detect TRIM28 expression. The correlation of TRIM28 with clinicopathological features was evaluated by Chi-square test. The relationship between TRIM28 expression and survival was further analyzed by the Kaplan-Meier and Cox regression method. A receiver operating characteristic (ROC) curve was used to assess the value of TRIM28 in predicting BC. Results In this retrospective research, it was demonstrated that TRIM28 was overexpressed in BC tissues. TRIM28 overexpression was correlated with lymph node metastasis, advanced TNM stage, and poor molecular subtype. The survival analysis showed that overall survival (OS) and progression-free survival (PFS) were significantly shorter in TRIM28-positive group. Moreover, TRIM28 was an independent prognostic factor for BC. And ROC analysis verified the diagnostic role of TRIM28 in BC. Conclusions TRIM28 is overexpressed in BC and might be a promising prognostic and diagnostic biomarker of BC.
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Jiang, Xuwen. "Genome-Wide Characterization and Expression Analysis of the Growth Regulating Factor (GRF) Gene Family in Strawberry (Fragaria vesca)." International Journal of Agriculture and Biology 25, no. 05 (2021): 1051–60. http://dx.doi.org/10.17957/ijab/15.1763.
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As one of the transcription factors only found in plants, the growth regulating factor (GRF) gene family has been reported in some plant species, but information on this gene family in strawberries remains unclear. Here, Fragaria vesca GRF (FvGRF) genes were systematically studied, including chromosomal location, gene structure, conserved motif, phylogenetic, expression profiling, post-transcriptional regulation, and functional analyses. The identified 10 FvGRFs were phylogenetically classified into two groups and five subgroups. Of these, nine FvGRFs were distributed on the five chromosomes, while FvGRF2 was located on the scf0512956. Motifs 2 and 1 corresponding to QLQ and WRC domains existed in all the FvGRF proteins. FvGRFs showed different expression patterns based on RT-qPCR analyses, for example, FvGRF1, FvGRF3, FvGRF6 and FvGRF8 were predominantly expressed in buds and blooming flowers, FvGRF4 and FvGRF5 were mainly expressed in young leaves, indicating that the roles of these genes are diverse and redundant in strawberry growth and development. Furthermore, FvGRF2 and FvGRF8 were experimentally validated to be the targets of strawberry miR396, suggesting the significance and conservation of miR396 in post-transcriptional regulation of FvGRFs. These results provide fundamental knowledge for further functional analyses of FvGRFs in strawberries. © 2021 Friends Science Publishers
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Brody, Stuart. "Circadian Rhythms in Fungi: Structure/Function/Evolution of Some Clock Components." Journal of Biological Rhythms 34, no. 4 (2019): 364–79. http://dx.doi.org/10.1177/0748730419852832.
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The fungal clock, especially that in Neurospora crassa, is composed of several proteins, notably FRQ, WC-1, and WC-2, which interact at the protein level and at the level of transcription. It is shown here that regions of the FRQ that are highly conserved in many fungal species show significant similarity to regions of proteins found in the amoebae Capsaspora and Acanthamoebae. These 2 amoebae were specifically explored because they have been suggested, based on extensive evidence, to be related to precursors of the modern fungi. Those proteins in Capsaspora/Acanthamoebae with some similarity to FRQ are LARP (an RNA-binding protein), ARNT (which has a PAS motif), and heat shock factor (HSF). These regions of LARP and HSF that show similarity to FRQ are highly conserved between plants, animals, and amoeba. This suggests that these regions were present at the time of the divergence of plants, fungi, insects, and animals, and therefore, they could be plausible precursors to regions of the fungal FRQ. These particular regions of FRQ that show similarity to LARP and HSF are also of functional significance since mutations in these regions of the Neurospora FRQ led to changes in the rhythm. The FRQ proteins from 13 different species of fungi were analyzed via motif analysis (MEME), and 11 different motifs were found. This provides some understanding as to the minimum requirements for an FRQ protein. Many of these FRQ motifs can be matched up with known domains in FRQ. In addition, these 13 different species of fungi were screened for the presence/absence of 7 additional genes/proteins that play some role in fungal clocks.
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Fang, Shengguo, and Qianghua Xu. "Variable number tandem repeats in the mitochondrial DNA Control region of the Chinese alligator, Alligator sinensis." Amphibia-Reptilia 27, no. 1 (2006): 93–101. http://dx.doi.org/10.1163/156853806776052038.
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AbstractVariable number tandem repeats (VNTRs) are present in the control region of mitochondrial DNA (mtDNA) of the alligatorid species; however, the evolutionary dynamics of the repetitive sequences and the significance of the VNTRs in the context of genetic monitoring of these species are not well explored. The Chinese alligator, Alligator sinensis is critically endangered and is now largely in captive breeding. Previous studies in mitochondrial genes revealed little genetic diversity existing within the populations. We reported here the structural variation and evolutionary features of mtVNTRs in the Changxing population of the species. The mtVNTRs contained 676∼785 base pairs, made up by 5 distinct motifs repeated 31∼36 times in 32 individuals examined. The motifs were 21∼22 nts in length, with high sequence similarity between each other and with those of the American alligator (Alligator mississippiensis), indicating origination of the mtVNTRs from a single ancestral duplication unit in both species. The 5′ and 3′ portions of the repetitive sequences in the Chinese alligator were very much conserved among the individuals, while those in the middle showed a higher degree of sequence variation. The frequency of each motif appearing in the mtVNTRs showed positive correlation to the binding energy of the potential secondary structure the motif could adopt. 17 VNTR types, of which, 6 from the second generation and 12 from the third generation were identified from the samples. Analysis of the multiple VNTR types showed a high level of stochastic mutation within each generation. The suitability of the mtVNTRs as a marker to monitor the genetic differentiation of the Chinese alligator was also discussed.
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Gorny, Miroslaw K., Constance Williams, Barbara Volsky, et al. "Cross-Clade Neutralizing Activity of Human Anti-V3 Monoclonal Antibodies Derived from the Cells of Individuals Infected with Non-B Clades of Human Immunodeficiency Virus Type 1." Journal of Virology 80, no. 14 (2006): 6865–72. http://dx.doi.org/10.1128/jvi.02202-05.
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ABSTRACT The majority of global human immunodeficiency virus infections are caused by viruses characterized by a GPGQ motif at the tip of the V3 loop. Characterization of anti-V3 monoclonal antibodies (MAbs) that neutralize isolates with the GPGQ V3 motif is an important step in designing vaccines that will induce such Abs. Consequently, seven human anti-V3 MAbs derived from the cells of individuals infected with non-B-subtype viruses (anti-V3non-B MAbs) were generated from the cells of individuals from Africa infected with circulating recombinant forms CRF02_AG, CRF09_cpx, and CRF13_cpx, each of which contains a subtype A env gene. Sequence analysis of plasma viruses revealed a GPGQ motif at the apex of the V3 loop from six of the seven subjects and a GPGR motif from one subject. The MAbs were selected with fusion proteins (FP) containing V392UG037.8 or V3JR-CSF from subtype A or B, respectively. In virus binding assays, five of the seven (71%) anti-V3non-B MAbs bound to V3-FPs from both subtype A and subtype B, while only four of the nine (44%) anti-V3B MAbs recognized both V3-FPs. Using two neutralization assays, both the anti-V3non-B and the anti-V3B MAbs neutralized subtype B viruses with similar activities, while the anti-V3non-B MAbs exhibited a tendency toward both increased potency and breadth of neutralization against non-B viruses compared to anti-V3B MAbs. Statistical significance was not achieved, due in large measure to the sizes of the MAb panels, but the overall pattern of data strongly suggests that viruses with the GPGQ motif at the tip of the V3 loop induce anti-V3 Abs with broader cross-neutralizing activity than do viruses with the GPGR motif.
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Parsch, John, Wolfgang Stephan, and Soichi Tanda. "A Highly Conserved Sequence in the 3′-Untranslated Region of the Drosophila Adh Gene Plays a Functional Role in Adh Expression." Genetics 151, no. 2 (1999): 667–74. http://dx.doi.org/10.1093/genetics/151.2.667.
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Abstract Phylogenetic analysis identified a highly conserved eight-base sequence (AAGGCTGA) within the 3′-untranslated region (UTR) of the Drosophila alcohol dehydrogenase gene, Adh. To examine the functional significance of this conserved motif, we performed in vitro deletion mutagenesis on the D. melanogaster Adh gene followed by P-element-mediated germline transformation. Deletion of all or part of the eight-base sequence leads to a twofold increase in in vivo ADH enzymatic activity. The increase in activity is temporally and spatially general and is the result of an underlying increase in Adh transcript. These results indicate that the conserved 3′-UTR motif plays a functional role in the negative regulation of Adh gene expression. The evolutionary significance of our results may be understood in the context of the amino acid change that produces the ADH-F allele and also leads to a twofold increase in ADH activity. While there is compelling evidence that the amino acid replacement has been a target of positive selection, the conservation of the 3′-UTR sequence suggests that it is under strong purifying selection. The selective difference between these two sequence changes, which have similar effects on ADH activity, may be explained by different metabolic costs associated with the increase in activity.
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Korzhova, I. N. "REVOLUTIONARY OR NEW? ROMANTICISM IN K. SIMONOV’s POEM “THE RETURN”." Bulletin of Udmurt University. Series History and Philology 31, no. 6 (2021): 1299–305. http://dx.doi.org/10.35634/2412-9534-2021-31-6-1299-1305.
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The article presents an analysis of Simonov's poem “The Return” in the aspect of interaction with the literary tradition. In the poem, the motifs and values of revolutionary romanticism, neo-romanticism and romanticism coexist in conflict. Thus, the romantic motif of flight structurally equates the city of childhood with a vulgar reality and calls into question the ideas of camaraderie and labor exploits that are important for Soviet literature. In the story of the hero's brief return to the city of his childhood, a "secondary phase of alienation" (Mann's term) is realized. The myth of the beloved as the embodiment of the heavenly ideal takes on special significance in the poem. The source of certain motifs and images is the romantic tradition as a whole, besides, allusions and quotations referring directly to the works of Byron, Zhukovsky, Pushkin and to the lyrics of Gumilev and Esenin based on the romantic heritage have been identified. The removal of the metaphysical vertical and the courageous optimism of the final part of the poem suggest that it belongs to neo-romanticism. This study allows us to clarify the idea of the aesthetic orientation of Simonov's early work.
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Fedorova, Irina. "THE TEMPTATION MOTIF IN THE OLD RUSSIAN APOCRYPHA "ZOSIMA’S JOURNEY TO THE RAHMANS"." Проблемы исторической поэтики 19, no. 4 (2021): 149–70. http://dx.doi.org/10.15393/j9.art.2021.10143.
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The article examines the functioning of the temptation motif in the ancient Russian apocrypha Zosima’s Journey to the Rahmans. The methods of implementing this motif in the text are analyzed; its significance in the plot of the work and in the formation of the image of the earthly paradise, with which the country of the blessed is associated in this literary work, is established. The biblical source of the motif is the Old Testament story of the fall of Adam and Eve and the test of the strength of faith, embodied in the temptation of Jesus Christ by the devil in the desert. The heterogenous structure of Zosima’s Journey to the Rahmans, where independent plots are integrated (the legendary story of the Rekhabites and the description of the land of the blessed), determined the varied realizations of the motif temptation in the text. An analysis revealed that the prologue of the literary work already contains an allusion to the Gospel temptation plot (a report of the forty-day prayer of the hermit to God). In the story of the Rechabites’ opposition to the king of Jerusalem and the story of the confrontation between Zosima and the devil, the motif of temptation is a plot-forming one. The story of the hermit’s temptation is formed by two storylines: Zosima's opposition to the devil and the fall of the first people, told by the tempter to intimidate the hermit. The Old Testament sin of Adam was developed in the storyline of Zosima and the Rechabite elder, who denounced the hermit as a «preacher» who involuntarily tried to persuade him to lie. The motif of temptation in Zosima’s Journey to the Rahmans may have been expressed explicitly, or merely be discernible, as in the story about the observance of Great Lent by the blessed or through the symbolic connotation of the numbers used in the literary work. The article also demonstrates that changes in the literary history of the apocrypha were reflected in the implementation of the temptation motif in its text.
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Odabashian, Mariette, Emanuela Carlotti, Shamzah Araf, et al. "Immunoglobulin Variable Region Gene Sequences Reveal N-Glycosylation Motifs As an Early and Stable Event in Follicular Lymphoma Pathology." Blood 132, Supplement 1 (2018): 4101. http://dx.doi.org/10.1182/blood-2018-99-112397.
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Abstract Introduction: Follicular lymphoma (FL) cells retain expression of a functional B cell receptor (BCR) despite the loss of one Ig allele due to the hallmark t14:18 translocation and ongoing somatic hypermutation (SHM) of the variable genes (V genes) which increases the likelihood of crippling mutations. SHM introduces N-glycosylation (N-gly) motifs within the V genes, a feature exclusively restricted to germinal centre (GC)-derived lymphomas. Oligosaccharides of the high mannose type are added to motifs and interact with calcium-dependent lectins associated with cells of the microenvironment. This activates the BCR signalling pathway and likely contributes to the survival, retention and proliferation of tumor cells in the GC. Determining at what stage of disease evolution N-gly motifs are acquired and their behaviour during progression can ascertain their importance in pathogenesis and their potential as an effective therapeutic target. To achieve this, we analysed motifs within the Ig heavy chain variable gene (IGHV) of tumor-related subclones across temporal FL samples. Method: Genomic DNA from three FL patients taken at different time points of disease progression were analysed. In total, 8 samples were selected, all carrying an IGHV3 rearranged tumor clone. IGHV DNA amplicons were sent for 2x250bp paired-end sequencing using the Miseq Illumina platform (Genewiz, NJ). Tumor-related reads with counts greater than ten were selected following analysis on IMGT/HIGH-V-QUEST. Reads were aligned and unique sequences were assigned as subclones. Additional tumor related reads sequenced on the Roche 454 Life Sciences Genome Sequencer FLX were available (Patients 4 & 5). Subclones were analysed for N-gly motifs and evolutionary pathways were generated using the IgTree program, based on intraclonal SHM profiles and homology of tumor clones to the germline IGHV sequence. Results: The earliest time point samples for Patient's 1, 3, 4 & 5 contained one N-gly site within the IGHV of the MC defined by the largest count number. These sites were conserved in >97% of unique subclones (p<0.0001) despite variations in the nucleotide sequence within the region as a result of ongoing SHM. This conservation included the most mutated subclones which had a mean SHM rate of 16.56%. Conservation was maintained across disease events. Patient 2 contained four N-gly sites located within the CDR1, FR2, CDR2, and FR3 regions. The first three sites were conserved in >97% of subclones in and across disease events, whereas the FR3 site was conserved in 95.5% of the diagnostic subclones and in ~80% of the relapsed and transformed populations. No subclones with loss of all four sites were detected for Patient 2. Patient 5 samples were taken from different anatomical sites with tumor populations acquiring distinct N-gly motifs, suggesting an early divergence in tumor evolution. Despite this, a minor population of motif positive clones are shared, suggesting a trafficking ability of subclones. Subclones with motifs made up ≥99% of the total tumor count, highlighting the motif as a feature of the tumor bulk, with motif negative clones representing a minor population. These negative clones are presumably lost during disease progression as they not shared between events. Evolutionary analysis revealed no additional sites are gained as motif positive clones expand while rare negative subclones cannot reacquire sites and do not undergo further diversification. Conclusion: We report for the first time that acquired N-gly motif sites are a clonal feature in FL disease as seen through their conservation both in the heterogeneous subclonal population and the overall tumor mass. The sites are also retained in progression-associated subclones while rare motif-negative subclones disappear. This suggests that although acquisition of additional driver mutations may dampen the tumor's microenvironment dependency, the motifs and added mannoses may retain functional significance at later stages of disease. The data indicates motifs as being a universal event of the reservoir cell pool responsible for propagating disease episodes. Targeting N-gly sites and their interacting partners may lead to the disruption of an early and vital FL-microenvironment interaction, presumably mediated through the mannose-lectin interaction, reducing relapse rates and progression of disease. Disclosures Forconi: Abbvie: Consultancy; Janssen-Cilag: Consultancy. Gribben:Abbvie: Honoraria; Roche: Honoraria; Pharmacyclics: Honoraria; Novartis: Honoraria; Cancer Research UK: Research Funding; Wellcome Trust: Research Funding; Acerta Pharma: Honoraria, Research Funding; TG Therapeutics: Honoraria; NIH: Research Funding; Kite: Honoraria; Janssen: Honoraria, Research Funding; Unum: Equity Ownership; Medical Research Council: Research Funding; Celgene: Consultancy, Honoraria, Research Funding.
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Ludin, B., K. Ashbridge, U. Funfschilling, and A. Matus. "Functional analysis of the MAP2 repeat domain." Journal of Cell Science 109, no. 1 (1996): 91–99. http://dx.doi.org/10.1242/jcs.109.1.91.
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The neuronal microtubule-associated protein MAP2 binds to microtubules via a domain near its C terminus containing a set of 3 or 4 imperfect repeats of a 31 amino acid motif. Using naturally occurring and mutated forms of the molecule containing between 1 and 4 repeats we have examined the contribution that these repeats make to MAP2 function and explored the significance of their repetition. The experiments utilised the short 3- and 4-repeat splice variants MAP2c and MAP2d that are expressed in developing neurons and in glia respectively, and mutant 1- and 2-repeat versions that were produced by using in vitro mutagenesis to remove further 31 amino acid units while leaving the rest of the molecule unaltered. The properties of these MAP2 variants were compared both with respect to their influence on microtubules in transfected non-neuronal cells and their ability to promote microtubule assembly in vitro. We found that each of the known effects of MAP2, including the bundling of microtubules and induction of process formation in living cells, are expressed by the 1-repeat form MAP2c3, which contains only the third repeat (R3). A second 1-repeat form, MAP2c4, which contains only R4, interacts more weakly with tubulin in vitro and does not bind to microtubules in transfected cells. The microtubule-related properties of MAP2 thus arise mainly from a single predominant repeat unit, R3. In vitro assembly experiments showed that the primary effect of all the repeats is to lower the critical concentration of tubulin required for microtubule assembly but that they differ greatly in potency. The results did not reveal a separate function related to the repetition of the repeat motifs, but instead suggest that its purpose is to tailor the efficiency of MAP2 to the cellular environment in which it has to function.
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Krupenina, Mariya I. "Eccentric characters in Dickens’s novel "David Copperfield" and the motif of premonition." Vestnik of Kostroma State University, no. 3 (2019): 67–71. http://dx.doi.org/10.34216/1998-0817-2019-25-3-67-71.
Full textAbstract:
The coming-of-age story "David Copperfield" by Charles Dickens is notable for its internal organisation, revealing the literary style of the author. Dickens’ serialised novels demonstrate a thoughtful unity of content and form. This makes it possible to speak of the existence of common components, making up his works. The unified tone of all Dickens’s works is reached by a special "touch" of the "fantastic", what has already been noted in literary criticism. The significance of the concept of "fancy" for creative work of this realist writer allows us paying attention to the most important "fantastic" structural component in "David Copperfield" – the so-called "premonition moments", experienced by the characters. Even if premonitions may seem incredible at the first mention, they are often justified in the course of action. An analysis of the episodes associated with the premonitions of the characters, both accurate and inaccurate, as well as those containing "fantastic" (fabulous, eccentric, theatrical) portraits, allows us demonstrating how exactly the writer’s individual manner of writing manifests itself.
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Solinger, Jachen A., Donatella Pascolini, and Wolf-Dietrich Heyer. "Active-Site Mutations in the Xrn1p Exoribonuclease of Saccharomyces cerevisiae Reveal a Specific Role in Meiosis." Molecular and Cellular Biology 19, no. 9 (1999): 5930–42. http://dx.doi.org/10.1128/mcb.19.9.5930.
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ABSTRACTXrn1p ofSaccharomyces cerevisiaeis a major cytoplasmic RNA turnover exonuclease which is evolutionarily conserved from yeasts to mammals. Deletion of theXRN1gene causes pleiotropic phenotypes, which have been interpreted as indirect consequences of the RNA turnover defect. By sequence comparisons, we have identified three loosely defined, common 5′-3′ exonuclease motifs. The significance of motif II has been confirmed by mutant analysis with Xrn1p. The amino acid changes D206A and D208A abolish singly or in combination the exonuclease activity in vivo. These mutations show separation of function. They cause identical phenotypes to that ofxrn1Δ in vegetative cells but do not exhibit the severe meiotic arrest and the spore lethality phenotype typical for the deletion. In addition,xrn1-D208Adoes not cause the severe reduction in meiotic popout recombination in a double mutant withdmc1as doesxrn1Δ. Biochemical analysis of the DNA binding, exonuclease, and homologous pairing activity of purified mutant enzyme demonstrated the specific loss of exonuclease activity. However, the mutant enzyme is competent to promote in vitro assembly of tubulin into microtubules. These results define a separable and specific function of Xrn1p in meiosis which appears unrelated to its RNA turnover function in vegetative cells.
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Widiyanti, Dhyani. "Fashion Lurik Kontemporer sebagai Hibriditas dalam Budaya Urban." Urban: Jurnal Seni Urban 3, no. 2 (2020): 91–98. http://dx.doi.org/10.52969/jsu.v3i2.34.
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Lurik is a fabric that has a stripe motif and is made with a non-machine loom (Alat Tenun Bukan Mesin - ATBM). Lurik’s stripes can be divided into three motifs, namely lajuran, pakan malang, and cacahan. In the beginning lurik was only worn in the palace circles, not just by anyone, especially common people. In its development, lurik becomes a general public consumption; especially among urbanites lurik is a means to build their identities. This research studies contemporary works in lurik fashion, which are hybridity between elements in traditional lurik and elements existing in the culture or lifestyle of urbanites in building their new identity; it is a combination of qualitative research and the utilization of literary exploration. The primary data objects are various examples of contemporary lurik, which are analysed through content analysis. The content analysis applied here is Homi Bhabha’s post colonialism, which is a part of the deconstructive postmodern text interpretation method. The results show the following: (1) contemporary lurik fashion is a fusion between elements representing Eastern culture, viz. lurik with lajuran motifs, pakan malang, and cacahan, with elements that represent Western culture, viz. long wrap dresses, midi dress, and semi billowy airy dress, (2) based on an elucidation of internal aspects, contemporary lurik fashion expresses a dualism in meaning, viz. the popular meanings that is the superficial appreciations enjoyed by the common people and the subliminal meanings indicating depth of lurik motifs the meaning of which are studied by people who understand their significance. (3) Based on the interpretation of external aspects, contemporary lurik fashion is a form of resistance to modern Western fashion as well as being a Keraton tradition. Posed against Western fashion, hybridity is used as a way to de-colonialize Western influences that are considered incompatible with Eastern culture. Meanwhile, in the perspective of Keraton tradition, hybridity is carried out as a form of desacralization so that lurik can be utilized by as many people as possible as an individual expression, (4) the hybridity in contemporary lurik fashion creates a new identity, namely its placement in urban spaces and lifestyles more broadly, especially in relation to its access in semi-formal environment.Lurik merupakan kain yang mempunyai motif garis-garis dan dibuat dengan alat tenun bukan mesin (ATBM). Motif garis-garis pada lurik dapat dibagi ke dalam tiga macam motif, yaitu lajuran, pakan malang, dan cacahan. Lurik sendiri pada awalnya hanya digunakan di keraton dan tidak boleh digunakan oleh sembarang orang apalagi rakyat biasa. Pada perkembangannya, lurik kemudian menjadi konsumsi umum terutama bagi kaum urban dalam membangun identitasnya. Penelitian ini mengkaji karya-karya fashion lurik kontemporer yang merupakan hibriditas antara unsur-unsur dalam lurik tradisional dengan unsur-unsur yang ada dalam budaya atau gaya hidup kaum urban dalam rangka membangun identitas baru yang merupakan hasil peleburan atau fusi. Penelitian ini menggunakan metode kualitatif dengan menggunakan data-data kepustakaan. Objek data primer ini adalah berbagai contoh busana lurik kontemporer untuk kemudian dianalisis dengan analisis konten. Analisis konten yang digunakan adalah dengan menggunakan poskolonialisme Homi Bhabha yang merupakan satu bagian dari metode tafsir teks posmodern dekonstruktif. Hasil penelitian kemudian menunjukkan hal-hal berikut ini: (1) fashion lurik kontemporer adalah peleburan atau fusi antara unsur yang merepresentasikan budaya Timur, yaitu lurik dengan motif lajuran, pakan malang, dan cacahan dengan unsur-unsur yang merepresentasikan budaya Barat, yaitu gaun panjang (long wrap dress), midi dress, dan gaun airy semi billowy, (2) berdasarkan interpretasi terhadap aspek internal, fashion lurik kontemporer melahirkan dualisme makna, yaitu makna populer yang cenderung dinikmati secara permukaan untuk diapresiasi orang awam dan makna subliminal yang menunjukkan adanya kedalaman pada motif-motif lurik yang digunakan untuk dikaji secara mendalam oleh orang yang paham makna lurik secara mendalam, (3) berdasarkan interpretasi terhadap aspek eksternal, fashion lurik kontemporer adalah bentuk resistensi terhadap fashion modern Barat sekaligus tradisi keraton. Terhadap fashion modern Barat, hibriditas dilakukan sebagai cara untuk dekolonialisasi terhadap pengaruh-pengaruh Barat yang dianggap tidak sesuai sepenuhnya dengan budaya Timur. Sementara terhadap tradisi keraton, hibriditas dilakukan sebagai bentuk desakralisasi agar lurik dapat dikonsumsi oleh sebanyak mungkin orang sebagai ekspresi individual, (4) hibriditas yang dilakukan pada fashion lurik kontemporer melahirkan identitas baru, yaitu penempatan lurik pada ruang dan gaya hidup urban secara lebih luas terutama terkait aksesnya pada situasi semiformal.
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Zaltariov, Mirela-Fernanda, Mihaela Turtoi, Dragos Peptanariu, et al. "Chemical Attachment of 5-Nitrosalicylaldimine Motif to Silatrane Resulting in an Organic–Inorganic Structure with High Medicinal Significance." Pharmaceutics 14, no. 12 (2022): 2838. http://dx.doi.org/10.3390/pharmaceutics14122838.
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Two chemical motifs of interest for medicinal chemistry, silatrane as 1-(3-aminopropyl) silatrane (SIL M), and nitro group attached in position 5 to salicylaldehyde, are coupled in a new structure, 1-(3-{[(2-hydroxy-5-nitrophenyl)methylidene]amino}propyl)silatrane (SIL-BS), through an azomethine moiety, also known as a versatile pharmacophore. The high purity isolated compound was structurally characterized by an elemental, spectral, and single crystal X-ray diffraction analysis. Given the structural premises for being a biologically active compound, different specific techniques and protocols have been used to evaluate their in vitro hydrolytic stability in simulated physiological conditions, the cytotoxicity on two cancer cell lines (HepG2 and MCF7), and protein binding ability—with a major role in drug ADME (Absorption, Distribution, Metabolism and Excretion), in parallel with those of the SIL M. While the latter had a good biocompatibility, the nitro-silatrane derivative, SIL-BS, exhibited a higher cytotoxic activity on HepG2 and MCF7 cell lines, performance assigned, among others, to the known capacity of the nitro group to promote a specific cytotoxicity by a “activation by reduction” mechanism. Both compounds exhibited increased bio- and muco-adhesiveness, which can favor an optimized therapeutic effect by increased drug permeation and residence time in tumor location. Additional benefits of these compounds have been demonstrated by their antimicrobial activity on several fungi and bacteria species. Molecular docking computations on Human Serum Albumin (HSA) and MPRO COVID-19 protease demonstrated their potential in the development of new drugs for combined therapy.
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Parida, Swarup K., Devendra K. Yadava, and Trilochan Mohapatra. "Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis." Genome 53, no. 1 (2010): 55–67. http://dx.doi.org/10.1139/g09-084.
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Microsatellites present in the transcribed regions of the genome have the potential to reveal functional diversity. Unigene sequence databases are the sources of such genic microsatellites with unique flanking sequences and genomic locations even in complex polyploids. The present study was designed to assay the unigenes of Brassica napus and B. rapa for various microsatellite repeats, and to design markers and use them in comparative genome analysis and study of evolution. The average frequency of microsatellites in Brassica unigenes was one in every 7.25 kb of sequence, as compared with one in every 8.57 kb of sequence in Arabidopsis thaliana . Trinucleotide motifs coding for serine and the dinucleotide motif GA were most abundant. We designed 2374 and 347 unigene-based microsatellite (UGMS) markers including 541 and 58 class I types in B. napus and B. rapa, respectively, and evaluated their use across diverse species and genera. Most of these markers (93.3%) gave successful amplification of target microsatellite motifs, which was confirmed by sequencing. Interspecific polymorphism between B. napus and B. rapa detected in silico for the UGMS markers was 4.16 times higher in 5′ untranslated regions than in coding sequences. Physical anchoring of Brassica UGMS markers on the A. thaliana genome indicated their significance in studying the evolutionary history of A. thaliana genomic duplications in relation to speciation. Comparative physical mapping identified 85% of Brassica unigenes as single copy and gave clues for the presence of conserved primordial gene order. Complex chromosomal rearrangements such as inversions, tandem and segmental duplications, and insertions/deletions were evident between A. thaliana and B. rapa genomes. The results obtained have encouraging implications for the use of UGMS markers in comparative genome analysis and for understanding evolutionary complexities in the family Brassicaceae.
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Patel, Navin B., Hetal I. Soni, and Rahul B. Parmar. "Significance of Microwave Irradiation in Synthesis of Thiazolidin-4-one Bearing Pyrimidine Analogues: Their in vitro Antimicrobial, Antituberculosis and Antimalarial Studies." Current Microwave Chemistry 7, no. 3 (2020): 230–37. http://dx.doi.org/10.2174/2213335607999200918155613.
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Aim: To synthesise biologically active thiazolidin-4-one by microwave irradiation method and evaluate against different species of bacteria, fungi and Plasmodium falciparum. Background: Microwave irradiation method is serviceable for rapid and sustainable synthesis. In this present study, Thiazolidin-4-one bearing pyrimidine derivatives have been synthesized by microwave irradiation method. Objective: Thiazolidin-4-one is a valuable motif because of its broad-spectrum biological evaluation. It is famous for many types of biological profiles, mainly antimicrobial, anti-tuberculosis, anti- convulsant, antihypertensive, hypoglycemic agent and antimalarial. This biological response leads our attention towards the change of Thiazolidin-4-one skeleton to enhance potential. Present study aims to carry out a rapid synthesis of Thiazolidin-4-one derivative of pyrimidine by microwave- assisted heating. Methods: 4-(4-substituted phenyl)-6-(substituted aryl) pyrimidin-2-amine was the key intermediate required for the synthesis of 3-(4-(Substituted phenyl)-6-(substituted aryl) pyrimidin-2-yl)-2-(4-hydroxy phenyl) thiozolidin-4-one (5A-J), which was prepared by using microwave irradiation. The structures of all newly synthesized motifs were characterized by spectral analysis (IR, 1H NMR, 13C NMR spectroscopy) and screened for antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pyogenes; antifungal activity against Candida albicans, Aspergillus niger, Aspergillus Clavatus; anti-tuberculosis activity against M. tuberculosis H37RV and antimalarial activity against Plasmodium falciparum. Results: Higher yield with less time-consuming method is the main advantage of Thiazolidin- 4-one bearing pyrimidine motifs synthesis. The excellent biological response of compounds 5B, 5C, 5D, 5G, 5H, 5I, and 5J was observed. Conclusion: As compared to conventional method, less time is required for the preparation of Thiazolidin- 4-one analogues by using advantageous microwave irradiation method. Thiazolidin-4-one derivatives showed improved biological activity.
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Christensen, Stephen L., Peter Cho, Amares Chatt, and Peng Zhang. "A site-specific comparative study of Au102 and Au25 nanoclusters using theoretical EXAFS and l-DOS." Canadian Journal of Chemistry 93, no. 1 (2015): 32–36. http://dx.doi.org/10.1139/cjc-2014-0271.
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Recent advances in Au–thiolate nanocluster synthesis have allowed the total structural determination of several nanoclusters by X-ray crystallography. The high-precision structural information of these nanoclusters enables atomic site-specific analysis of local structure and electronic character. In this work, a site-specific comparative study of Au102(SR)44 and Au25(SR)18 was conducted to elucidate the size and site effects on the local environment and electronic character of their common surface structural unit, the –SR–Au–SR–Au–SR– “double-staple” motif. Simulation of the pseudo-radial distribution function from extended X-ray absorption fine structure (EXAFS) shows a significant difference in their local environments despite their identical geometric shape. Local density of states (l-DOS) calculations consistently reveal the difference in their electronic characters for gold d-electron density and d-DOS position. These differences are then related to the unique aurophilic interactions and size- or site-dependent electronic character of Au atoms in the double-staple motif. The differing local structure and electronic behaviour of the “double-staple” motif in Au102(SR)44 and Au25(SR)18 highlight the significance of both size and site effects on the surface structure and electronic property of Au–thiolate nanoclusters. The theoretical results may also be useful in the interpretation of future experimental XAFS and X-ray photoelectron spectroscopy (XPS) data of these nanoclusters.
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Toshchakov, Vladimir Y., and Andrew F. Neuwald. "Evolutionary conserved sequence patterns that determine functional specialization of metazoan TIR domains." Journal of Immunology 204, no. 1_Supplement (2020): 79.7. http://dx.doi.org/10.4049/jimmunol.204.supp.79.7.
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Abstract Toll-Interleukin-1R Resistance (TIR) domains represent a type of protein fold ubiquitously present in all forms of cellular life. The TIR domains are present in functionally and architecturally diverse proteins. A large subgroup of metazoan TIRs is involved in signaling that initiate and regulate the immune response elicited by infection or damaged self. This study applies Bayesian partitioning with pattern selection (BPPS) to classify the TIR domains based on sequence patterns that best distinguish individual groups. The algorithm was applied to &gt;26000 phylogenetically diverse TIR domain sequences selected for non-redundancy from publicly available protein sequence banks. The analysis has revealed 10 metazoan groups, nine of which comprise either orthologous proteins or a protein family. Available structural data suggest that the identified groups may be uniquely characterized by regional backbone fold variants, which can be associated with a corresponding group-specific sequence motif. In addition to these fold-defining motifs, the BPPS also identified groups of surface-exposed residues conserved in TIRAP and MyD88 orthologs, which correspond to predicted sites that mediate the signal-dependent TIR oligomerization. This analysis also has clarified the functional significance of locally conserved sequence motifs, named Box 2 and Box 3, as each of these motifs is a part of a larger block of conserved, intramolecularly interacting residues. Finally, this study has identified the sequence patterns that differentiate TIRs of different classes, such TIRs of TLRs, from TIRs of the IL-1R family, or their adapter proteins, and highlights the differences between metazoan, plant, and bacterial TIRs.
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Purwanto, Aldi, Ira Hidayati, and Abdul Qohar. "Hubungan Persepsi Terhadap Organisasi dan Motif Sosial dengan Minat Berorganisasi." ANFUSINA: Journal of Psychology 5, no. 1 (2022): 73–80. http://dx.doi.org/10.24042/ajp.v5i1.13987.
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IInterest in organization is the existence of interest from students to participate in and choose to be active in an organization that makes a person have a tendency to pay attention to the activities of the organization he chooses based on encouragement from within. Perceptions of the organization and social motives are factors that influence the occurrence of organizational interest. This study aims to determine the relationship between perceptions of organization and social motives with organizational interest in the ushuluddin faculty and religious studies. Researchers used quantitative research methods with precision sampling techniques and the samples in this study were 70 students who joined the Study Program Student Association (HMPS). Data collection techniques in this study used a psychological scale including a scale of organizational interest, perception of the organization and social motives. The scale of organizational interest is 21 items (α = 0.905), the perception of the organization is 21 items (α = 0.880), and the social motive is 19 items (α = 0.866). The analysis technique used is a multiple regression analysis technique assisted by the SPSS 21.0 for windows program. The analyzed data shows the results: The results showed that the value of Rx1.2.3-y = 0.542, the value of F = 13.951 on the significance of p = 0.000 and stated (p 0.01). The results obtained that the perception of the organization and social motives provide an effective contribution of 29.4% to the dependent variable and 70.6% generated by other variables outside the study. Based on the calculation results obtained the value of rx1-y = 0.459 and p = 0.000 (p 0.05). The results obtained indicate that there is a relationship between perceptions of the organization and interest in the organization. The results obtained stated that the perception variable towards the organization received an effective contribution of 16.7% to the interest in organization. Based on the calculation results obtained the value of rx2-y = 0.418 and p = 0.000 (p 0.05). The results obtained indicate that there is a relationship between social motives and organizational interest. The results obtained stated that the social motive variable received an effective contribution of 12.7% to organizational interest. Keywords: Interest in Organization, Perception of Organization, and social motives
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Wang, Duan, Xuan Zhang, Xiangmei Yao, Peng Zhang, Rongxiang Fang, and Jian Ye. "A 7-Amino-Acid Motif of Rep Protein Essential for Virulence Is Critical for Triggering Host Defense Against Sri Lankan Cassava Mosaic Virus." Molecular Plant-Microbe Interactions® 33, no. 1 (2020): 78–86. http://dx.doi.org/10.1094/mpmi-06-19-0163-fi.
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Geminiviruses cause severe damage to agriculture worldwide. The replication (Rep) protein is the indispensable viral protein for viral replication. Although various functional domains of Rep protein in Geminivirus spp. have been characterized, the most carboxyl terminus of Rep protein was not available. We have reported the first cassava-infecting geminivirus, Sri Lankan cassava mosaic virus (SLCMV-HN7 strain), in China. In this study, we reported the second Chinese SLCMV strain, SLCMV-Col, and conducted comparative genomic analysis between these two SLCMV strains. The virulence of SLCMV-Col is much stronger than SLCMV-HN7, indicated by the higher virus titer, more severe symptoms, and more extent host defense. We functionally characterized that Rep protein, a 7-amino-acid motif at the most carboxyl terminus, is essential for Rep protein accumulation and virulence of SLCMV. We also provided evidence suggesting that the motif could also enhance triggering of salicylic acid (SA) defense against SLCMV infection in Nicotiana benthamiana. The significance of the balance between virulence and host SA defense responses in expanding invasions of SLCMV is also discussed.
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HUA, Len V., Kiyoshi HIDAKA, Xavier PESESSE, Larry D. BARNES, and Stephen B. SHEARS. "Paralogous murine Nudt10 and Nudt11 genes have differential expression patterns but encode identical proteins that are physiologically competent diphosphoinositol polyphosphate phosphohydrolases." Biochemical Journal 373, no. 1 (2003): 81–89. http://dx.doi.org/10.1042/bj20030142.
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We previously described paralogous human genes {NUDT10 and NUDT11 [where NUDT is (nucleoside diphosphate attached moiety ‘X’)-type motif, also known as the ‘nudix’-type motif]} encoding type 3 diphosphoinositol polyphosphate phosphohydrolases (DIPP3) [Hidaka, Caffrey, Hua, Zhang, Falck, Nickel, Carrel, Barnes and Shears (2002) J. Biol. Chem. 277, 32730–32738]. Normally, gene duplication is redundant, and lacks biological significance. Is this true for the DIPP3 genes? We address this question by characterizing highly-conserved murine Nudt10 and Nudt11 homologues of the human genes. Thus these genes must have been duplicated prior to the divergence of primates and sciurognath rodents, approx. 115 million years ago, greatly exceeding the 4 million year half-life for inactivation of redundant paralogues; our data therefore indicate that the DIPP3 duplication is unusual in being physiologically significant. One possible functional consequence is gene neofunctionalization, but we exclude that, since Nudt10 and Nudt11 encode identical proteins. Another possibility is gene subfunctionalization, which we studied by conducting the first quantitative expression analysis of these genes. We demonstrated high Nudt10 expression in liver, kidney and testis; Nudt11 expression is primarily restricted to the brain. This differential, but complementary, expression pattern indicates that subfunctionalization is the evolutionary consequence of DIPP3 gene duplication. Our kinetic data argue that diphosphoinositol polyphosphates are more physiologically relevant substrates for DIPP3 than are either diadenosine hexaphosphate or 5-phosphoribosyl 1-pyrophosphate. Thus the significance of the Nudt10/Nudt11 duplication is specific hydrolysis of diphosphoinositol polyphosphates in a tissue-dependent manner.