Journal articles: 'I-Motifs'

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Shamim, Amen, Maria Razzaq, and Kyeong Kyu Kim. "MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif." International Journal of Molecular Sciences 22, no. 1 (December 23, 2020): 61. http://dx.doi.org/10.3390/ijms22010061.

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I-Motif is a tetrameric cytosine-rich DNA structure with hemi-protonated cytosine: cytosine base pairs. Recent evidence showed that i-motif structures in human cells play regulatory roles in the genome. Therefore, characterization of novel i-motifs and investigation of their functional implication are urgently needed for comprehensive understanding of their roles in gene regulation. However, considering the complications of experimental investigation of i-motifs and the large number of putative i-motifs in the genome, development of an in silico tool for the characterization of i-motifs in the high throughput scale is necessary. We developed a novel computation method, MD-TSPC4, to predict the thermal stability of i-motifs based on molecular modeling and molecular dynamic simulation. By assuming that the flexibility of loops in i-motifs correlated with thermal stability within certain temperature ranges, we evaluated the correlation between the root mean square deviations (RMSDs) of model structures and the thermal stability as the experimentally obtained melting temperature (Tm). Based on this correlation, we propose an equation for Tm prediction from RMSD. We expect this method can be useful for estimating the overall structure and stability of putative i-motifs in the genome, which can be a starting point of further structural and functional studies of i-motifs.

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Jiang, Guimei, Lijun Xu, Kewei Wang, Xing Chen, Jine Wang, Weiguo Cao, and Renjun Pei. "Quinaldine red as a fluorescent light-up probe for i-motif structures." Analytical Methods 9, no. 10 (2017): 1585–88. http://dx.doi.org/10.1039/c7ay00301c.

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We report a new fluorescent probe for i-motif structures. When binding to i-motifs, quinaldine red exhibits a remarkable increase in its fluorescence, which benefits i-motif-involved label-free systems.

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Ruggiero, Emanuela, Sara Lago, Primož Šket, Matteo Nadai, Ilaria Frasson, Janez Plavec, and Sara N. Richter. "A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription." Nucleic Acids Research 47, no. 21 (October 29, 2019): 11057–68. http://dx.doi.org/10.1093/nar/gkz937.

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Abstract I-motifs are non-canonical nucleic acids structures characterized by intercalated H-bonds between hemi-protonated cytosines. Evidence on the involvement of i-motif structures in the regulation of cellular processes in human cells has been consistently growing in the recent years. However, i-motifs within non-human genomes have never been investigated. Here, we report the characterization of i-motifs within the long terminal repeat (LTR) promoter of the HIV-1 proviral genome. Biophysical and biochemical analysis revealed formation of a predominant i-motif with an unprecedented loop composition. One-dimensional nuclear magnetic resonance investigation demonstrated formation of three G-C H-bonds in the long loop, which likely improve the structure overall stability. Pull-down experiments combined with mass spectrometry and protein crosslinking analysis showed that the LTR i-motif is recognized by the cellular protein hnRNP K, which induced folding at physiological conditions. In addition, hnRNP K silencing resulted in an increased LTR promoter activity, confirming the ability of the protein to stabilize the i-motif-forming sequence, which in turn regulates the LTR-mediated HIV-1 transcription. These findings provide new insights into the complexity of the HIV-1 virus and lay the basis for innovative antiviral drug design, based on the possibility to selectively recognize and target the HIV-1 LTR i-motif.

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Martins, Alexandra, Christian H. Gross, and Stewart Shuman. "Mutational Analysis of Vaccinia Virus Nucleoside Triphosphate Phosphohydrolase I, a DNA-Dependent ATPase of the DExH Box Family." Journal of Virology 73, no. 2 (February 1, 1999): 1302–8. http://dx.doi.org/10.1128/jvi.73.2.1302-1308.1999.

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ABSTRACT Vaccinia virus nucleoside triphosphate phosphohydrolase I (NPH-I) is a DNA-dependent ATPase that serves as a transcription termination factor during viral mRNA synthesis. NPH-I is a member of the DExH box family of nucleic acid-dependent nucleoside triphosphatases (NTPases), which is defined by the presence of several conserved sequence motifs. We have assessed the contributions of individual amino acids (underlined) in motifs I (GxGKT), II (DExHN), III (SAT), and VI (QxxGRxxR) to ATP hydrolysis by performing alanine scanning mutagenesis. Significant decrements in ATPase activity resulted from mutations at nine positions: Lys-61 and Thr-62 (motif I); Asp-141, Glu-142, His-144, and Asn-145 (motif II); and Gln-472, Arg-476, and Arg-479 (motif VI). Structure-function relationships at each of these positions were clarified by introducing conservative substitutions and by steady-state kinetic analysis of the mutant enzymes. Comparison of our findings for NPH-I with those of mutational studies of other DExH and DEAD box proteins underscores similarities as well as numerous disparities in structure-activity relationships. We conclude that the functions of the conserved amino acids of the NTPase motifs are context dependent.

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Nufer, Oliver, Svend Guldbrandsen, Martin Degen, Felix Kappeler, Jean-Pierre Paccaud, Katsuko Tani, and Hans-Peter Hauri. "Role of cytoplasmic C-terminal amino acids of membrane proteins in ER export." Journal of Cell Science 115, no. 3 (February 1, 2002): 619–28. http://dx.doi.org/10.1242/jcs.115.3.619.

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Export of membrane proteins from the ER is believed to be selective and require transport signals, but the identity of such signals has remained elusive. The recycling type I membrane protein ERGIC-53 carries a C-terminal diphenylalanine motif that is required for efficient ER export. Here we show that this motif can be functionally substituted by a single phenylalanine or tyrosine at position -2, two leucines or isoleucines at position -1 and -2 or a single valine at position -1. These motifs are common among mammalian type I membrane proteins. A single C-terminal valine, but none of the other motifs,accelerates transport of inefficiently exported reporter constructs and hence operates as an export signal. The valine signal is position, but not context,dependent. All transport motifs mediate COPII binding in vitro with distinct preferences for the COPII subunits Sec23p, Sec24Bp, Sec24Cp and p125. These results suggest that cytoplasmic C-terminal amino-acid motifs, either alone or in conjunction with other transport determinants, accelerate ER export of numerous type I and probably polytopic membrane proteins by mediating interaction with COPII coat components.

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Saha, Puja, Deepanjan Panda, Diana Müller, Arunabha Maity, Harald Schwalbe, and Jyotirmayee Dash. "In situ formation of transcriptional modulators using non-canonical DNA i-motifs." Chemical Science 11, no. 8 (2020): 2058–67. http://dx.doi.org/10.1039/d0sc00514b.

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Grote, Johanna, Beate Neumann, Hans-Georg Stammler, and Norbert W. Mitzel. "Diversity of aggregation motifs in gold(i) dithiocarboxylate complexes." Dalton Transactions 47, no. 13 (2018): 4701–6. http://dx.doi.org/10.1039/c8dt00342d.

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Molecular structures and aggregation motifs of different substituted gold(i) dithiocarboxylate complexes are presented and a correlation between the substituent and the aggregation motif is discussed.

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Grote, Johanna, Beate Neumann, Hans-Georg Stammler, and Norbert W. Mitzel. "Silver(i) dithiocarboxylate complexes – clustering and aggregation." Dalton Transactions 47, no. 17 (2018): 6036–40. http://dx.doi.org/10.1039/c8dt00279g.

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Molecular structures and aggregation motifs of a series of neutral homoleptic silver(i) dithiocarboxylate are presented and a correlation between the substituent and aggregation motif as well as the differences from the (almost) analogous gold(i) complexes are discussed.

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Yanti Pantur, Mariani Irma, and Ika Ismurdiyahwati. "Songke Fabric in Libo, Wela Kaweng and Su'i Motif from Perak Village, Manggarai Regency, East Nusa Tenggara, in Study of Visual Aesthetics of Meaning and Function." IMAGIONARY 1, no. 2 (April 30, 2023): 76–82. http://dx.doi.org/10.51353/jim.v1i2.753.

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Songke fabrics with libo, wela kaweng and su'I motifs are a type of Indonesian textile work. Songke cloth with libo, wela kaweng and su'I motifs is a textile work from Perak village, Manggarai Regency, East Nusa Tenggara. This research takes the topic of the libo, wela kaweng and suâ€™I motifs on songke cloth in Perak village, Manggarai Regency, because these motifs are superior motifs that are often produced and a cultural heritage that has its own meaning and function. Therefore, this study aims to determine the visual aesthetic meaning and function of songke cloth in libo, wela kaweng and su'I motifs on songke cloth. The data sources in this study are the figures of songke cloth craftsmen, the village head, and cultural observers. This type of research uses descriptive qualitative with an explanation through the data obtained from data collection using the method of observation, documentation, and direct interviews. The results of this study show that the libo motif means the relationship between humans and the natural surroundings where in everyday life humans always need water to sustain life. The wela kaweng motif means a plant that can be used as medicine to heal and treat livestock wounds in ancient times and the suâ€™I motifs means as a bridge that separates the customs between the tribes in the Silver Village. Songke fabrics with libo, wela kaweng and su'I motifs are used by the Manggarai community in attending traditional ceremonies such as engagements, weddings, penti (year-end thanks giving or every harvest) and funerals.

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Leporcq, Clémentine, Yannick Spill, Delphine Balaramane, Christophe Toussaint, Michaël Weber, and Anaïs Flore Bardet. "TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions." Nucleic Acids Research 48, W1 (April 23, 2020): W208—W217. http://dx.doi.org/10.1093/nar/gkaa252.

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Abstract Transcription factors (TFs) regulate the expression of gene expression. The binding specificities of many TFs have been deciphered and summarized as position-weight matrices, also called TF motifs. Despite the availability of hundreds of known TF motifs in databases, it remains non-trivial to quickly query and visualize the enrichment of known TF motifs in genomic regions of interest. Towards this goal, we developed TFmotifView, a web server that allows to study the distribution of known TF motifs in genomic regions. Based on input genomic regions and selected TF motifs, TFmotifView performs an overlap of the genomic regions with TF motif occurrences identified using a dynamic P-value threshold. TFmotifView generates three different outputs: (i) an enrichment table and scatterplot calculating the significance of TF motif occurrences in genomic regions compared to control regions, (ii) a genomic view of the organisation of TF motifs in each genomic region and (iii) a metaplot summarizing the position of TF motifs relative to the center of the regions. TFmotifView will contribute to the integration of TF motif information with a wide range of genomic datasets towards the goal to better understand the regulation of gene expression by transcription factors. TFmotifView is freely available at http://bardet.u-strasbg.fr/tfmotifview/.

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Wright, Elisé P., Mahmoud A. S. Abdelhamid, Michelle O. Ehiabor, Melanie C. Grigg, Kelly Irving, Nicole M. Smith, and Zoë A. E. Waller. "Epigenetic modification of cytosines fine tunes the stability of i-motif DNA." Nucleic Acids Research 48, no. 1 (November 28, 2019): 55–62. http://dx.doi.org/10.1093/nar/gkz1082.

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Abstract i-Motifs are widely used in nanotechnology, play a part in gene regulation and have been detected in human nuclei. As these structures are composed of cytosine, they are potential sites for epigenetic modification. In addition to 5-methyl- and 5-hydroxymethylcytosine modifications, recent evidence has suggested biological roles for 5-formylcytosine and 5-carboxylcytosine. Herein the human telomeric i-motif sequence was used to examine how these four epigenetic modifications alter the thermal and pH stability of i-motifs. Changes in melting temperature and transitional pH depended on both the type of modification and its position within the i-motif forming sequence. The cytosines most sensitive to modification were next to the first and third loops within the structure. Using previously described i-motif forming sequences, we screened the MCF-7 and MCF-10A methylomes to map 5-methylcytosine and found the majority of sequences were differentially methylated in MCF7 (cancerous) and MCF10A (non-cancerous) cell lines. Furthermore, i-motif forming sequences stable at neutral pH were significantly more likely to be epigenetically modified than traditional acidic i-motif forming sequences. This work has implications not only in the epigenetic regulation of DNA, but also allows discreet tunability of i-motif stability for nanotechnological applications.

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HAMAHATA, Akiko, Yoshimi TAKATA, Tomoharu GOMI, and Motoji FUJIOKA. "Probing the S-adenosylmethionine-binding site of rat guanidinoacetate methyltransferase. Effect of site-directed mutagenesis of residues that are conserved across mammalian non-nucleic acid methyltransferases. Effect of site-directed mutagenesis of residues that are conserved across mammalian non-nucleic acid methyltransferases." Biochemical Journal 317, no. 1 (July 1, 1996): 141–45. http://dx.doi.org/10.1042/bj3170141.

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Most mammalian non-nucleic acid methyltransferases share three sequence motifs. To gain insight into the S-adenosylmethionine (AdoMet)-binding site of guanidinoacetate methyltransferase, we mutated several conserved residues that are found in or near motifs I and II. Conversion of either of two glycine residues of motif I (Gly67 and Gly69) to an alanine resulted in an inactive enzyme. These enzymes, although having UV absorption, fluorescence and far-UV CD spectra virtually identical with those of the wild-type enzyme, seem to be conformationally different from the wild-type enzyme as judged by near-UV CD spectra and the extent of urea denaturation, and are apparently not capable of binding AdoMet. Mutation of Tyr136 of motif II to a valine resulted in a decrease in kcat/Km values for substrates. Changing this residue to a phenylalanine caused only a minor change in kcat/Km for AdoMet. This suggests that the aromatic side chain stabilizes the binding of AdoMet. Mutagenic changes of Glu89, which is the residue corresponding to the conserved acidic residue on the C-terminal side of motif I, indicated its contribution to AdoMet binding. These results are consistent with the idea that both motifs I and II are crucial in forming the AdoMet binding site of guanidinoacetate methyltransferase.

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Kisbali, Tamás Péter. "“LUDUS NATURAE”: SHELLS AS SCULPTED MOTIFS IN ANCIENT GREEK ART." RSUH/RGGU Bulletin. "Literary Theory. Linguistics. Cultural Studies" Series 1 (2023): 155–68. http://dx.doi.org/10.28995/2686-7249-2023-1-155-168.

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In this article, I trace the various ways Ancient Greek artisans used seashell-motifs, and how they interpreted these natural forms in artistic contexts. The reason for the popularity of seashells lies in their visual and haptic variety, their wealth of association, and the device of something secret hidden under the hard outer shell. I examine three possible variants of the motif’s treatment in relief and volume: the shell-container as part of a vessel, the shell as an independent container, the shell as a sculpted motif on a vessel. Of particular interest are the vases where the integration of shell and vessel is especially marked, such as plastic aryballoi, lekythoi and other types (often with the inclusion of mythological subjects, such as the birth of Aphrodite). Terracotta and metal pyxides are also considered. Alongside these, I examine the rare “marble shells”, stone vessels carved in the intricate shape of “pelican’s foot” shells.

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Sahu, Santosh Kumar, Himadri Gourav Behuria, Sangam Gupta, and Babita Sahoo. "Sequence Analysis of a Subset of Plasma Membrane Raft Proteome Containing CXXC Metal Binding Motifs." International Journal of Knowledge Discovery in Bioinformatics 5, no. 2 (July 2015): 1–15. http://dx.doi.org/10.4018/ijkdb.2015070101.

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In an attempt to identify the metal sensing proteins localized to mammalian plasma membrane, the authors screened a list of 300 raft associated proteins that are involved in cellular signaling mechanisms by searching the presence of metal thionin (CXXC) motifs. 50 proteins were found to possess CXXC motifs that could act as potential metal sensing proteins. The authors determined membrane topologies of the above CXXC motif containing proteins using TM-pred and analyzed the positions of their transmembrane (TM) domains using Bio-edit software. Based on the topology of CXXC domains, the authors classified all the raft-associated metal sensing proteins into six categories. They are (i) Exoplasmic tails with CXXC motif, (ii) Exoplasmic loops with CXXC motif, (iii) Cytosolic tails with CXXC motif, (iv) Cytosolic loop with CXXC motif, (v) TM domains with CXXC motifs, (vi) Proteins with multiple topologies of CXXC motif. The authors' study will lead to understanding of the raft-mediated mechanism of heavy metal sensing and signaling in mammalian cells.

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Goldhahn, Joakim. "Kosmologiska mantlar – strödda tankar kring hällbildsforskningens primitiva arv och epistemologi jämte bronsålderns kosmologi." In Situ Archaeologica 5 (December 31, 2003): 9–41. http://dx.doi.org/10.58323/insi.v5.12706.

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This article was originally presented at the 8th Nordic Bronze Age Seminar, held at the National Museum in Copenhagen back in 2000. It focuses on rock art interpretation in general and the history of research and interpretation of the so-called “cap” motifs in particular. Today, eleven different cap motifs are known in Scandinavia. I argue that researchers often tend to focus, isolate and overemphasise different single rock art motifs, or categories of motifs, and their connotations in an essentialistic search of their meaning. To put it simple: A cap is interpreted as a cap. It is also argued that this simplistic interpretation is related to a functionalistic research tradition that was formulated in the late 19th and early 20th century. This research tradition was challenged by Jarl Nordbladh during the 1970s and his structuralistic prolegomena. Inspired by the latter perspective, and some anthropological case studies, I hope to be able to show that the meaning of a single rock art motif is not imbedded in the motifs themselves, nor their connotation per se. In my own approach to the cap motifs, I include other motifs, and relate the images to the mythological birth and rebirth of the sun and how this is expressed at some open air sites and in the closed burial context in Sagaholm, Kivik and Klinta. The article ends with a suggestion that there are several ways to express meaning through the use of rock art. A cap is not always a cap.

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Korvin, Gábor. "Muḥammad’s Jug: Arabic Motifs in Borges’s Texts." Arabist: Budapest Studies in Arabic 46 (2024): 103–47. http://dx.doi.org/10.58513/arabist.2024.46.4.

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In this study I discuss twenty-three Arabic motifs in Borges’s texts and trace them back to their most likely sources. Borges did not know Arabic and gained his knowledge of the Orient from secondary sources, books by Burton, Lane, Asín Palacios, and others. In many cases Borges playfully changed these Arabic motifs, or invented new ones. In the rare occasions when he gave his sources, these were as fantastic as the stories themselves: references to non-existing tomes by non-existing scholars, to an odd book of Burton (instead of the correct one by Lane), or to an out-of-context citation from Gibbon. I succeeded in locating the sources of most of these motifs and proved for a few others that they are inventions of Borges. I could not find the source of one poem. For one motif (“Iskander’s mirror”) I could only show that it is well-documented in Oriental literature, but I could not find any likely source where Borges could have learned about it.

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Solleder, Marthe, Philippe Guillaume, Julien Racle, Justine Michaux, Hui-Song Pak, Markus Müller, George Coukos, Michal Bassani-Sternberg, and David Gfeller. "Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands." Molecular & Cellular Proteomics 19, no. 2 (December 17, 2019): 390–404. http://dx.doi.org/10.1074/mcp.tir119.001641.

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The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-translational modifications. To fill this gap, we curated phosphorylated HLA-I ligands from several immunopeptidomics studies (including six newly measured samples) covering 72 HLA-I alleles and retrieved a total of 2,066 unique phosphorylated peptides. We then expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands. Our results reveal a clear enrichment of phosphorylated peptides among HLA-C ligands and demonstrate a prevalent role of both HLA-I motifs and kinase motifs on the presentation of phosphorylated peptides. These data further enabled us to develop and validate the first predictor of interactions between HLA-I molecules and phosphorylated peptides.

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Maslova, Anna G. "Biblical Motifs and Images in E. I. Kostrov’s Poetry." Проблемы исторической поэтики 27, no. 1 (February 2020): 92–110. http://dx.doi.org/10.15393/j9.art.2020.6882.

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The article analyzes the peculiarities of biblical motifs and images in E. I. Kostrov’s works. In his odes the poet often refers to the Old Testament scenes and images through the prism of a Christian aspect. Kostrov considers ancient and the Old Testament subjects in the light of the Christian and Orthodox tradition. The poet attributes a Christian sound to the secular genre of the ode, saturating his works with the motifs of the Holy Scriptures. Kostrov often uses the concept of “meekness” emphasizing the sanctity of the Orthodox power, which gets commandments of mercy and humility from God leading to spiritual salvation. The motif of two paths — the unholy and righteous ones — becomes cross-cutting in Kostrov’s poetry. The path of Russia corresponds to the latter one. The motif of divine light descending into the world and eradicating the darkness is the motif of the people “chosen by God”. According to Kostrov, not the Jews but the Russians are such a people. Working with the texts of the Psalms, Kostrov introduces his own motifs, shows his individuality, reveals his own experiences and doubts, and disagrees with some ideas of his era. Christian ideals of meekness and non-violence are the main values in E. I. Kostrov’s poetry.

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Irving, Kelly L., Jessica J. King, Zoë A. E. Waller, Cameron W. Evans, and Nicole M. Smith. "Stability and context of intercalated motifs (i-motifs) for biological applications." Biochimie 198 (July 2022): 33–47. http://dx.doi.org/10.1016/j.biochi.2022.03.001.

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Maziyah, Siti. "Motif Batik Tegal: Pengaruh Mataram, Pesisiran dan Islam." Endogami: Jurnal Ilmiah Kajian Antropologi 1, no. 2 (June 8, 2018): 177. http://dx.doi.org/10.14710/endogami.1.2.177-193.

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BATIK -- motif is one of the cultural results that can show the identity of the region and has a unique cultural background. This article highlights the issue of Tegal Batik motif. What kind of batik Tegal is ? What cultures are behind the Tegal batik motifs? I apply the research method with historical approach to find the history of Tegal. Who are the actors in carrying out cultural changes in Tegal, especially related to the emergence of batik motifs. Based on the history, it will be known why Tegal batik has such motives. The results showed that based on the history of Tegal, batik motifs get influence from some other cultural areas besides the Tegal community itself, namely from the Kingdom of Mataram and from the Pasisiran region. In addition, batik motifs Tegal also get a strong influence from “wong kaji”, namely the Muslim traders that taft with the Islam included in describing to the batik motifs. Again, there is one type of batik produced by rural communities of Tegal, called “folk-batik”.

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Chakraborty, Saikat, and Yamuna Krishnan. "Kinetic hybrid i-motifs: Intercepting DNA with RNA to form a DNA2–RNA2 i-motif." Biochimie 90, no. 7 (July 2008): 1088–95. http://dx.doi.org/10.1016/j.biochi.2008.02.022.

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Thuillard, Marc. "Analysis of the Worldwide Distribution of the ‘Man or Animal in the Moon’ Motifs." Folklore: Electronic Journal of Folklore 84 (December 2021): 127–44. http://dx.doi.org/10.7592/fejf2021.84.thuillard.

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For millennia, people have seen a man, an animal, or an object as they look at the moon. The motif of the ‘frog/toad in the Moon’ was recorded in writing in the Book of Changes (I Ching) over 2400 years ago. The ‘man in the Moon’ theme is found in old Norse literature in the Younger Edda. In Mesoamerica, the story of the ‘rabbit in the Moon’ is pre-Columbian. This study analyses the different versions by combining areal studies as well as structural and statistical analyses with information from ancient texts and archaeological artefacts. In particular, I compare the geographic distribution of the main motifs to the 2,278 motifs in Yuri Berezkin’s database. In this context, I report on the observed similarities between the geographic distribution of the ‘man or animal in the Moon’ motifs and the two of the most widespread earth creation myths.

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Wenzel, Jürgen J., Heidi Rossmann, Christian Fottner, Stefan Neuwirth, Carolin Neukirch, Peter Lohse, Julia K. Bickmann, et al. "Identification and Prevention of Genotyping Errors Caused by G-Quadruplex– and i-Motif–Like Sequences." Clinical Chemistry 55, no. 7 (July 1, 2009): 1361–71. http://dx.doi.org/10.1373/clinchem.2008.118661.

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Abstract Background: Reliable PCR amplification of DNA fragments is the prerequisite for most genetic assays. We investigated the impact of G-quadruplex– or i-motif–like sequences on the reliability of PCR-based genetic analyses. Methods: We found the sequence context of a common intronic polymorphism in the MEN1 gene (multiple endocrine neoplasia I) to be the cause of systematic genotyping errors by inducing preferential amplification of one allelic variant [allele dropout (ADO)]. Bioinformatic analyses and pyrosequencing-based allele quantification enabled the identification of the underlying DNA structures. Results: We showed that G-quadruplex– or i-motif–like sequences can reproducibly cause ADO. In these cases, amplification efficiency strongly depends on the PCR enzyme and buffer conditions, the magnesium concentration in particular. In a randomly chosen subset of candidate single-nucleotide polymorphisms (SNPs) defined by properties deduced from 2 originally identified ADO cases, we confirmed preferential PCR amplification in up to 50% of the SNPs. We subsequently identified G-quadruplex and i-motifs harboring a SNP that alters the typical motif as the cause of this phenomenon, and a genomewide search based on the respective motifs predicted 0.5% of all SNPs listed by dbSNP and Online Mendelian Inheritance in Man to be potentially affected. Conclusions: Undetected, the described phenomenon produces systematic errors in genetic analyses that may lead to misdiagnoses in clinical settings. PCR products should be checked for G-quadruplex and i-motifs to avoid the formation of ADO-causing secondary structures. Truly affected assays can then be identified by a simple experimental procedure, which simultaneously provides the solution to the problem. .

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Barry, Barbara. ""Where's my Fool?": Lear Motifs in Rigoletto." Comparative Drama 46, no. 1 (2012): 57–96. http://dx.doi.org/10.1353/cdr.2012.0001.

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Shi, Lili, Pai Peng, Jiao Zheng, Qiwei Wang, Zhijin Tian, Huihui Wang, and Tao Li. "I-Motif/miniduplex hybrid structures bind benzothiazole dyes with unprecedented efficiencies: a generic light-up system for label-free DNA nanoassemblies and bioimaging." Nucleic Acids Research 48, no. 4 (January 17, 2020): 1681–90. http://dx.doi.org/10.1093/nar/gkaa020.

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Abstract I-motif DNAs have been widely employed as robust modulating components to construct reconfigurable DNA nanodevices that function well in acidic cellular environments. However, they generally display poor interactivity with fluorescent ligands under these complex conditions, illustrating a major difficulty in utilizing i-motifs as the light-up system for label-free DNA nanoassemblies and bioimaging. Towards addressing this challenge, here we devise new types of i-motif/miniduplex hybrid structures that display an unprecedentedly high interactivity with commonly-used benzothiazole dyes (e.g. thioflavin T). A well-chosen tetranucleotide, whose optimal sequence depends on the used ligand, is appended to the 5′-terminals of diverse i-motifs and forms a minimal parallel duplex thereby creating a preferential site for binding ligands, verified by molecular dynamics simulation. In this way, the fluorescence of ligands can be dramatically enhanced by the i-motif/miniduplex hybrids under complex physiological conditions. This provides a generic light-up system with a high signal-to-background ratio for programmable DNA nanoassemblies, illustrated through utilizing it for a pH-driven framework nucleic acid nanodevice manipulated in acidic cellular membrane microenvironments. It enables label-free fluorescence bioimaging in response to extracellular pH change.

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Rose, Nicola J., and Andrew M. L. Lever. "The rapamycin sensitivity of human T-cell leukaemia virus type I-induced T-cell proliferation is mediated independently of the polypyrimidine motifs in the 5′ long terminal repeat." Journal of General Virology 82, no. 2 (February 1, 2001): 435–39. http://dx.doi.org/10.1099/0022-1317-82-2-435.

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The immunosuppressant rapamycin can regulate the translation of a subset of messenger RNAs, a phenotype which has been linked to the presence of a polypyrimidine motif [C(N)4–14] downstream of the mRNA cap structure. T-cell clones naturally infected with transcriptionally active human T-cell leukaemia virus, type I (HTLV-I) undergo autologous proliferation; this phenotype is inhibited by rapamycin but not FK506, which reverses the rapamycin effect. Within the R region of the HTLV-I 5′ long terminal repeat (LTR) there are seven polypyrimidine motifs. We sought to determine if these were involved in the sensitivity of proliferation to the presence of rapamycin. Here we illustrate the generation of an in vitro model of this rapamycin-sensitivity and the analysis of LTR mutants which were created to determine the importance of the polypyrimidine motifs. Reporter gene assays suggest the effect is independent of the polypyrimidine motifs in the virus leader sequence.

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Day, Henry Albert, Elisé Patricia Wright, Colin John MacDonald, Andrew James Gates, and Zoë Ann Ella Waller. "Reversible DNA i-motif to hairpin switching induced by copper(ii) cations." Chemical Communications 51, no. 74 (2015): 14099–102. http://dx.doi.org/10.1039/c5cc05111h.

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i-Motif forming DNA sequences have previously been used for many different nanotechnological applications, but all have used changes in pH to fold the DNA. Here it is shown that Cu(ii) cations can be used to re-fold i-motifs into hairpin structures, without changing the pH.

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Davenport, Miles P., Katherine J. Smith, Dan Barouch, Scott W. Reid, Wanda M. Bodnar, Anthony C. Willis, Donald F. Hunt, and Adrian V. S. Hill. "HLA Class I Binding Motifs Derived from Random Peptide Libraries Differ at the COOH Terminus from Those of Eluted Peptides." Journal of Experimental Medicine 185, no. 2 (January 20, 1997): 367–72. http://dx.doi.org/10.1084/jem.185.2.367.

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Recombinant HLA-A2, HLA-B8, or HLA-B53 heavy chain produced in Escherichia coli was combined with recombinant β2-microglobulin (β2m) and a pool of randomly synthesised nonamer peptides. This mixture was allowed to refold to form stable major histocompatability complex (MHC) class I complexes, which were then purified by gel filtration chromatography. The peptides bound to the MHC class I molecules were subsequently eluted and sequenced as a pool. Peptide binding motifs for these three MHC class I molecules were derived and compared with previously described motifs derived from analysis of naturally processed peptides eluted from the surface of cells. This comparison indicated that the peptides bound by the recombinant MHC class I molecules showed a similar motif to naturally processed and presented peptides, with the exception of the peptide COOH terminus. Whereas the motifs derived from naturally processed peptides eluted from HLA-A2 and HLA-B8 indicated a strong preference for hydrophobic amino acids at the COOH terminus, this preference was not observed in our studies. We propose that this difference reflects the effects of processing or transport on the peptide repertoire available for binding to MHC class I molecules in vivo.

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Brzeski, J., T. Grycuk, A. W. Lipkowski, W. Rudnicki, B. Lesyng, and A. Jerzmanowski. "Binding of SPXK- and APXK-peptide motifs to AT-rich DNA. Experimental and theoretical studies." Acta Biochimica Polonica 45, no. 1 (March 31, 1998): 221–31. http://dx.doi.org/10.18388/abp.1998_4304.

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The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK-type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.

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Liu, Mingfu, Raymond J. Turner, Tara L. Winstone, Andrea Saetre, Melanie Dyllick-Brenzinger, Glen Jickling, Leslie W. Tari, Joel H. Weiner, and Diane E. Taylor. "Escherichia coli TehB RequiresS-Adenosylmethionine as a Cofactor To Mediate Tellurite Resistance." Journal of Bacteriology 182, no. 22 (November 15, 2000): 6509–13. http://dx.doi.org/10.1128/jb.182.22.6509-6513.2000.

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ABSTRACT The Escherichia coli chromosomal determinant for tellurite resistance consists of two genes (tehA andtehB) which, when expressed on a multicopy plasmid, confer resistance to K2TeO3 at 128 μg/ml, compared to the MIC of 2 μg/ml for the wild type. TehB is a cytoplasmic protein which possesses three conserved motifs (I, II, and III) found in S-adenosyl-l-methionine (SAM)-dependent non-nucleic acid methyltransferases. Replacement of the conserved aspartate residue in motif I by asparagine or alanine, or of the conserved phenylalanine in motif II by tyrosine or alanine, decreased resistance to background levels. Our results are consistent with motifs I and II in TehB being involved in SAM binding. Additionally, conformational changes in TehB are observed upon binding of both tellurite and SAM. The hydrodynamic radius of TehB measured by dynamic light scattering showed a ∼20% decrease upon binding of both tellurite and SAM. These data suggest that TehB utilizes a methyltransferase activity in the detoxification of tellurite.

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Jones, Christopher M. "“The Wealth of Nations Shall Come to You”: Light, Tribute, and Implacement in Isaiah 60." Vetus Testamentum 64, no. 4 (September 22, 2014): 611–22. http://dx.doi.org/10.1163/15685330-12341178.

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I draw on spatial theory, and particularly Edward Casey’s concept of “implacement,” to investigate the rhetoric of Isaiah 60. Implacement means being concretely placed. I argue that Isaiah 60 uses the motifs of light and tribute to “implace” Jerusalem for its audience. It uses these motifs to acknowledge Jerusalem’s degraded state in the early fifth century and to imagine the means by which the city’s restoration will occur. Drawing on Wells’ work on inner-Isaianic allusion and Strawn’s argument that Isa 60 incorporates and subverts Persian iconography, I argue that, in Isa 60, the motif of light implaces Jerusalem by marking it out as the cosmic center and by drawing the nations to the city. The motif of tribute, meanwhile, actually transfers the implacedness of the nations to Jerusalem. The rhetoric of the text encourages its audience to re-imagine the Jerusalem of their experience in its restored and glorified future state.

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Delgado, Julio, Hernando Escobar, David Crockett, Eduardo Reyes-Vargas, and Peter Jensen. "Analysis of the performance of peptide predicting methods using MHC class I peptide sequencing in the C57BL/6 mouse (78.11)." Journal of Immunology 182, no. 1_Supplement (April 1, 2009): 78.11. http://dx.doi.org/10.4049/jimmunol.182.supp.78.11.

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Abstract MHC class I peptide-binding motifs can defined by sequencing of peptides naturally bound to MHC class I molecules. More recently MHC class I-peptide binding motifs have be defined on the basis of quantitative MHC-peptide binding assays in vitro using peptide libraries. The information on peptide binding motifs obtained using binding assays have been useful to develop numerous bioinformatics-based tools to predict the binding of peptides to MHC class I molecules. To date few studies have analyzed the performance of these bioinformatics tools to predict peptides determined by sequencing of peptides eluted directly from MHC class I molecules. In this study we performed sequencing of endogenous peptides eluted from H2Kb and Db molecules expressed in the C57BL/6 mouse. Using data from 280 H2-class I-bound peptides we identified novel preferred anchor residues located in H2Kb and H2Db-associated peptides. When comparing the predicting affinity performance of 3 bioinformatics tools we found that between 60 to 95% of peptides eluted from H2Kb and H2Db molecules were correctly classified as binders by these 3 predicting algorithms, suggesting that these bioinformatics tools are reliable and efficient for prediction of naturally processed MHC class I ligands. These results expand our knowledge about H2 class I binding specificities and provide the identity of positions that can be used for better characterization of H2 class I peptide-binding motifs. Similar studies using sensitive methods for sequencing large numbers of peptides from other MHC molecules are needed to establish more precise motif information that can be used for the training of bioinformatics tool employed in the prediction of CD8 T-cell epitopes

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Nakashima, Yoshiki, Hiroki Iguchi, Kenta Takakura, Yuta Nakamura, Kenji Izumi, Naoya Koba, Satoshi Haneda, and Masayoshi Tsukahara. "Adhesion Characteristics of Human Pancreatic Islets, Duct Epithelial Cells, and Acinar Cells to a Polymer Scaffold." Cell Transplantation 31 (January 2022): 096368972211205. http://dx.doi.org/10.1177/09636897221120500.

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We reported in 2018 that among several extracellular matrices, fibronectin, type I collagen, type IV collagen, laminin I, fibrinogen, and bovine serum albumin, fibronectin is particularly useful for adhesion of porcine pancreatic tissue. Subsequently, we developed a technology that enables the chemical coating of the constituent motifs of fibronectin onto cell culture dishes. In this experiment, we used islets (purity ≥ 90%), duct epithelial cells (purity ≥ 60%), and acinar cells (purity ≥ 99%) isolated from human pancreas according to the Edmonton protocol published in 2000 and achieved adhesion to the constituent motifs of fibronectin. A solution including cGMP Prodo Islet Media was used as the assay solution. In islets, adhesion was enhanced with the constitutive motifs of fibronectin compared with uncoated islets. In the functional evaluation of islets, insulin mRNA expression and insulin secretion were enhanced by the constitutive motif of fibronectin compared with non-coated islets. The stimulation index was comparable between non-coated islets and fibronectin motifs. In duct epithelial cells, adhesion was mildly promoted by the fibronectin component compared with non-coated component, while in acinar cells, adhesion was inhibited by the fibronectin component compared with the non-coated component. These data suggest that the constitutive motifs of fibronectin are useful for the adhesion of islets and duct epithelial cells.

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Wildeman, A. G., M. Zenke, C. Schatz, M. Wintzerith, T. Grundström, H. Matthes, K. Takahashi, and P. Chambon. "Specific protein binding to the simian virus 40 enhancer in vitro." Molecular and Cellular Biology 6, no. 6 (June 1986): 2098–105. http://dx.doi.org/10.1128/mcb.6.6.2098-2105.1986.

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HeLa cell nuclear extracts and wild-type or mutated simian virus 40 enhancer DNA were used in DNase I footprinting experiments to study the interaction of putative trans-acting factors with the multiple enhancer motifs. We show that these nuclear extracts contain proteins that bind to these motifs. Because point mutations which are detrimental to the activity of a particular enhancer motif in vivo specifically prevent protection of that motif against DNase I digestion in vivo, we suggest that the bound proteins correspond to trans-acting factors involved in enhancement of transcription. Using mutants in which the two domains A and B of the simian virus 40 enhancer are either separated by insertion of DNA fragments or inverted with respect to their natural orientation, we also demonstrate that the trans-acting factors bind independently to the two domains.

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Wildeman, A. G., M. Zenke, C. Schatz, M. Wintzerith, T. Grundström, H. Matthes, K. Takahashi, and P. Chambon. "Specific protein binding to the simian virus 40 enhancer in vitro." Molecular and Cellular Biology 6, no. 6 (June 1986): 2098–105. http://dx.doi.org/10.1128/mcb.6.6.2098.

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HeLa cell nuclear extracts and wild-type or mutated simian virus 40 enhancer DNA were used in DNase I footprinting experiments to study the interaction of putative trans-acting factors with the multiple enhancer motifs. We show that these nuclear extracts contain proteins that bind to these motifs. Because point mutations which are detrimental to the activity of a particular enhancer motif in vivo specifically prevent protection of that motif against DNase I digestion in vivo, we suggest that the bound proteins correspond to trans-acting factors involved in enhancement of transcription. Using mutants in which the two domains A and B of the simian virus 40 enhancer are either separated by insertion of DNA fragments or inverted with respect to their natural orientation, we also demonstrate that the trans-acting factors bind independently to the two domains.

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Bielecka, Patrycja, Anna Dembska, and Bernard Juskowiak. "Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC." Molecules 24, no. 5 (March 8, 2019): 952. http://dx.doi.org/10.3390/molecules24050952.

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The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of tC fluorophore occurred upon lowering the pH from 8.0 to 5.5. Furthermore, we present and discuss fluorescence spectra of systems containing tC-modified i-motifs and complementary G-rich sequences in the ratios 1:1, 1:2, and 1:3 in response to pH changes. The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence. The possibility of using of the sensor for monitoring pH changes was demonstrated.

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Gross, Christian H., and Stewart Shuman. "The Nucleoside Triphosphatase and Helicase Activities of Vaccinia Virus NPH-II Are Essential for Virus Replication." Journal of Virology 72, no. 6 (June 1, 1998): 4729–36. http://dx.doi.org/10.1128/jvi.72.6.4729-4736.1998.

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ABSTRACT Vaccinia virus NPH-II is the prototypal RNA helicase of the DExH box protein family, which is defined by six shared sequence motifs. The contributions of conserved amino acids in motifs I (TGVGKTSQ), Ia (PRI), II (DExHE), and III (TAT) to enzyme activity were assessed by alanine scanning. NPH-II-Ala proteins were expressed in baculovirus-infected Sf9 cells, purified, and characterized with respect to their RNA helicase, nucleic acid-dependent ATPase, and RNA binding functions. Alanine substitutions at Lys-191 and Thr-192 (motif I), Arg-229 (motif Ia), and Glu-300 (motif II) caused severe defects in RNA unwinding that correlated with reduced rates of ATP hydrolysis. In contrast, alanine mutations at His-299 (motif II) and at Thr-326 and Thr-328 (motif III) elicited defects in RNA unwinding but spared the ATPase. None of the mutations analyzed affected the binding of NPH-II to RNA. These findings, together with previous mutational studies, indicate that NPH-II motifs I, Ia, II, and VI (QRxGRxGRxxxG) are essential for nucleoside triphosphate (NTP) hydrolysis, whereas motif III and the His moiety of the DExH-box serve to couple the NTPase and helicase activities. Wild-type and mutant NPH-II-Ala genes were tested for the ability to rescue temperature-sensitive nph2-tsviruses. NPH-II mutations that inactivated the phosphohydrolase in vitro were lethal in vivo, as judged by the failure to recover rescued viruses containing the Ala substitution. The NTPase activity was necessary, but not sufficient, to sustain virus replication, insofar as mutants for which NTPase was uncoupled from unwinding (H299A, T326A, and T328A) were also lethal. We conclude that the phosphohydrolase and helicase activities of NPH-II are essential for virus replication.

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Heavin, Joshua. "Seon Yong Kim. Curse Motifs in Galatians." Bulletin for Biblical Research 32, no. 2 (July 1, 2022): 243–48. http://dx.doi.org/10.5325/bullbiblrese.32.2.0243.

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Izquierdo, Adrian. ":La traduction fictive: Motifs d’un topos romanesque." Sixteenth Century Journal 53, no. 3 (September 1, 2022): 815–17. http://dx.doi.org/10.1086/scj5303120.

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Ramírez Caballero, Lisbeth, Christoph Kny, Regina Treudler, Jan C. Simon, Karolin Kern, Uta Jappe, and Michael Szardenings. "Identification of Seasonal Variations of Antibodies against PR-10-Specific Epitopes Can Be Improved Using Peptide-Phage Display." International Archives of Allergy and Immunology 181, no. 12 (2020): 919–25. http://dx.doi.org/10.1159/000509995.

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Background: In pollinosis patients, allergen-specific antibody titers show seasonal variations. Little is known about these variations at the epitope level. Objectives: We aimed at investigating seasonal variations on the level of allergen epitope recognition in patients with Bet v 1-related food allergy using a peptide phage display approach. Methods: Serum samples collected over 1 year from 4 patients of the placebo arm of the birch-associated soya allergy immunotherapy trial were included. To identify epitopes from Bet v 1-related food allergens, patient sera were used in peptide phage display experiments. In silico analysis of enriched allergen-related motifs was performed. Results: We identified epitope motifs related to Bet v 1 and its homologs in soya and hazelnut (Gly m 4 and Cor a 1, respectively) that were enriched in accordance with birch and hazel pollen exposure. Within several weeks after the birch pollen season peak, the pattern of identified epitope motifs differed considerably among patients. Data for amino acid preferences in homologous Bet v 1 and Cor a 1 epitope motifs identified for one of the investigated patients suggest changes in concentration or specificity of serum antibodies for the Cor a 1 epitope motif. Conclusions: Peptide phage display data suggest an impact of birch and hazel pollen exposure on the recognition pattern of Bet v 1-like allergen epitopes. Epitope-oriented analyses could provide deeper, personalized details regarding the allergen epitope recognition influenced by pollen exposure beyond the capability of current methods.

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Grishaeva, Tatiana M., Darya Kulichenko, and Yuri F. Bogdanov. "Bioinformatical analysis of eukaryotic shugoshins reveals meiosis-specific features of vertebrate shugoshins." PeerJ 4 (November 30, 2016): e2736. http://dx.doi.org/10.7717/peerj.2736.

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BackgroundShugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction and segregation. The study focused on the structural differences among SGOs acting during mitosis and meiosis that cause differences in chromosome behavior in these two types of cell division in different organisms.MethodsA bioinformatical analysis of protein domains, conserved amino acid motifs, and physicochemical properties of 32 proteins from 25 species of plants, fungi, and animals was performed.ResultsWe identified a C-terminal amino acid motif that is highly evolutionarily conserved among the SGOs protecting centromere cohesion of sister chromatids in meiotic anaphase I, but not among mitotic SGOs. This meiotic motif is arginine-rich in vertebrates. SGOs differ in different eukaryotic kingdoms by the sets and locations of amino acid motifs and the number of α-helical regions in the protein molecule.DiscussionThese structural differences between meiotic and mitotic SGOs probably could be responsible for the prolonged SGOs resistance to degradation during meiotic metaphase I and anaphase I. We suggest that the “arginine comb” in C-end meiotic motifs is capable of interaction by hydrogen bonds with guanine bases in the minor groove of DNA helix, thus protecting SGOs from hydrolysis. Our findings support independent evolution of meiosis in different lineages of multicellular organisms.

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Litvinov, Rustem I., Marco Mravic, Hua Zhu, John W. Weisel, William F. DeGrado, and Joel S. Bennett. "Unique transmembrane domain interactions differentially modulate integrin αvβ3 and αIIbβ3 function." Proceedings of the National Academy of Sciences 116, no. 25 (June 3, 2019): 12295–300. http://dx.doi.org/10.1073/pnas.1904867116.

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Lateral transmembrane (TM) helix–helix interactions between single-span membrane proteins play an important role in the assembly and signaling of many cell-surface receptors. Often, these helices contain two highly conserved yet distinct interaction motifs, arranged such that the motifs cannot be engaged simultaneously. However, there is sparse experimental evidence that dual-engagement mechanisms play a role in biological signaling. Here, we investigate the function of the two conserved interaction motifs in the TM domain of the integrin β3-subunit. The first motif uses reciprocating “large-large-small” amino acid packing to mediate the interaction of the β3 and αIIb TM domains and maintain the inactive resting conformation of the platelet integrin αIIbβ3. The second motif, S-x3-A-x3-I, is a variant of the classical “G-x3-G” motif. Using site-directed mutagenesis, optical trap-based force spectroscopy, and molecular modeling, we show that S-x3-A-x3-I does not engage αIIb but rather mediates the interaction of the β3 TM domain with the TM domain of the αv-subunit of the integrin αvβ3. Like αIIbβ3, αvβ3 on circulating platelets is inactive, and in the absence of platelet stimulation is unable to interact with components of the subendothelial matrix. However, disrupting any residue in the β3 S-x3-A-x3-I motif by site-directed mutations is sufficient to induce αvβ3 binding to the αvβ3 ligand osteopontin and to the monoclonal antibody WOW-1. Thus, the β3-integrin TM domain is able to engage in two mutually exclusive interactions that produce alternate α-subunit pairing, creating two integrins with distinct biological functions.

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Strobel, S. A. "Biochemical identification of A-minor motifs within RNA tertiary structure by interference analysis." Biochemical Society Transactions 30, no. 6 (November 1, 2002): 1126–31. http://dx.doi.org/10.1042/bst0301126.

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A-minor motifs are the most common tertiary structural elements in RNA helix packing. Biochemical identification of these interactions is now feasible using interference mapping analysis with the adenosine analogues 2′-deoxyadenosine and 3-deaza-adenosine. This approach was used to demonstrate that A-minor motifs mediate helix packing interactions that are important for 5′-splice site selection in the group I intron. By analysing the interference pattern of several analogues it is possible to identify and distinguish the four variants of the A-minor motif.

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Bresnahan, Patricia A., Wes Yonemoto, and Warner C. Greene. "Cutting Edge: SIV Nef Protein Utilizes Both Leucine- and Tyrosine-Based Protein Sorting Pathways for Down-Regulation of CD4." Journal of Immunology 163, no. 6 (September 15, 1999): 2977–81. http://dx.doi.org/10.4049/jimmunol.163.6.2977.

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Abstract The Nef protein is unique to primate lentiviruses and is closely linked to accelerated pathogenesis in both human and monkey hosts. Nef acts to down-regulate CD4 and MHC class I, two receptors important for immune function. A recent report demonstrated the presence of two tyrosine motifs in SIV Nef that contribute to its ability to down-regulate CD4 and to associate with clathrin adaptors. These tyrosine motifs are not present in HIV-1 Nef, which instead utilizes a leucine-based motif for its down-regulation of CD4. We now report that SIV Nef also contains a conserved leucine-based motif that contributes to CD4 down-regulation, functions to stimulate internalization, and contributes to the association of SIV Nef with clathrin adaptors AP-1 and AP-2. These results demonstrate that SIV Nef differs from HIV-1 Nef by its ability to use two parallel pathways of the protein-sorting machinery based on either tyrosine or leucine motifs.

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Nadia Hasna, Safira Rizqi, and Mein Kharnolis. "Penerapan Motif Batik Papua dengan Teknik Bordir pada Busana Pengantin Wanita." BAJU: Journal of Fashion & Textile Design Unesa 2, no. 1 (July 17, 2022): 18–23. http://dx.doi.org/10.26740/baju.v2n1.p18-23.

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Motif batik Papua yang berasal dari ragam hias khas Papua yang menjadi inspirasi dalam pembuatan busana pengantin wanita. Tujuan penelitian adalah untuk mengetahui proses dan hasil jadi penerapan motif batik papua dengan teknik bordir dibusana pengantin wanita. Metode yang digunakan adalah Double Diamond, yang terdiri dari 4 tahapan yaitu dicover, define, develop dan deliver. Dari hasil yang diperoleh, motif batik papua yaitu motif suku asmat yang diwujudkan teknik bordir digunakan sebagai detail di busana pengantin wanita. Proses pembuatan dengan cara membordir dengan mengikuti motif / pola yang telah di stilasi yang kemudian digambar atau dijiplak pada permukaan kain organza dan yang kemudian hasil bordiran kemudian dijadikan hiasan busana pengantin wanita. Hasil jadi pada busana pengantin wanita sesuai dengan ide perancangan antara lain menggunakan siluet I. Model busana pengantin wanita two piece yaitu gaun dan ekor lepas pasang. Penerapan bordir yang berbentuk motif batik Papua pada bagian bawah busana diterapkan dengan cara mapping dipermukaan busana yang menjadi hiasan dari look pada busana pengantin wanita. Hasil jadi busana secara keseluruhan telah memenuhi beberapa kriteria prinsip desain. Papuan batik motifs derived from Papuan decorative motifs are the inspiration for making bride's clothing. The purpose of the study was to determine the process and results of applying Papuan batik motifs with embroidery techniques in the bride's dress. The method used is Double Diamond, which consists of 4 stages, namely covered, define, develop and deliver. From the results obtained, the Papuan batik motif, namely the Asmat ethnic motif, is realized by embroidery techniques and is used as a detail in the bride's clothing. The process of making embroidery by following a stylized motif/pattern, drawn or traced on the surface of the organza cloth and then embroidered. The finished results on the bride's clothing are by the design idea, among others, using silhouette I. The bride's clothing model is two pieces, namely the dress and the loose tail. The application embroidery in the form of Papua batik motifs on the bottom of the dress is applied, mapping the surface of the clothing, which is the decoration of the look of the bride's attire. The finished product as a whole has met several design principles criteria.

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Choudhury, Manisha, Vijayan Viswanathan, Ajay Kumar Timiri, Barij Nayan Sinha, Venkatesan Jayaprakash, and Devadasan Velmurugan. "Crystal structures of 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(2,4-dimethylphenyl)acetamide and 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(3-methoxyphenyl)acetamide." Acta Crystallographica Section E Crystallographic Communications 73, no. 7 (June 13, 2017): 996–1000. http://dx.doi.org/10.1107/s2056989017008143.

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In the title compounds, C14H17N5OS (I) and C13H15N5O2S (II), the dihedral angle between the pyrimidine and benzene rings is 58.64 (8)° in (I) and 78.33 (9)° in (II). In both compounds, there is an intramolecular C—H...O hydrogen bond, and in (II) there is also an intramolecular N—H...N hydrogen bond present. In the crystals of both compounds, a pair of N—H...N hydrogen bonds links the individual molecules to form inversion dimers withR22(8) ring motifs. In (I), the dimers are linked by N—H...O and C—H...O hydrogen bonds, enclosingR21(14),R21(11) andR21(7) ring motifs, forming layers parallel to the (100) plane. There is also an N—H...π interaction present within the layer. In (II), the inversion dimers are linked by N—H...O hydrogen bonds enclosing anR44(18) ring motif. The presence of N—H...O and C—H...O hydrogen bonds generate anR21(6) ring motif. The combination of these various hydrogen bonds results in the formation of layers parallel to the (1-11) plane.

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Belodedova, Margarita G. "“YOU PICK UP WHAT COMES TO MIND”. CONNECTED MOTIFS IN THE LULLABIES OF THE RUSSIAN NORTH." RSUH/RGGU Bulletin. "Literary Theory. Linguistics. Cultural Studies" Series, no. 6 (2023): 51–63. http://dx.doi.org/10.28995/2686-7249-2023-6-51-63.

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Traditional lullabies do not have a common plot – they are a bundle of a number of micro-plots that the performer “pulls” together, each time creating a new song. Each lullaby will be unique not only in the volume of the text, but also in the number of motifs, their coiled-uncoiled, their combination and sequence. Despite the improvisational nature of the genre, lullabies consist of motifs so stable and have such a rigid and clichéd rhythmic structure that these motifs can be called formulas. They can have both a rather capacious, brief form, and a more expanded structure – one of these forms of motifs the performer chooses during the creation, singing of the lullaby, and depending on the chosen form he chooses subsequent motifs belonging to the same “cluster”. Since the duration of the lullaby depends entirely on the addressee (i. e., on how long it will take him to fall asleep), there is no rigid order regulating the sequence of motif selection. Nevertheless, it is possible to trace some recurring “associations” – bundles of motifs that are more often next to each other.

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Gupta, Akshay. "An Intra-Hindu Comparative Analysis of Caitanya Vaiṣṇavism’s Eco-Theological Motifs." Journal of Dharma Studies 4, no. 1 (April 2021): 5–27. http://dx.doi.org/10.1007/s42240-021-00098-y.

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AbstractIn the midst of the earth’s pressing climate catastrophe, the nexus between ecology and religion merits further investigation. In this article, I attempt to illuminate certain important aspects of this nexus by analyzing various Hindu eco-theological motifs, with a particular focus on those of the Hindu religious tradition known as Caitanya Vaiṣṇavism. I will compare and contrast the eco-theological motifs of Caitanya Vaiṣṇavism with those of other notable Hindu religious traditions and texts. Ultimately, I attempt to demonstrate that certain Caitanya Vaiṣṇava eco-theological motifs can, when properly interpreted and applied, serve as valuable environmentally oriented conceptual resources. I also argue that these eco-theological motifs can offset some of the conceptual pitfalls that limit the effectiveness of various pan-Hindu eco-theological motifs as conceptual resources for environmental amelioration. Although the Caitanya Vaiṣṇava eco-theological framework is not without conceptual hurdles, I nevertheless maintain that Caitanya Vaiṣṇava eco-theological motifs are worthy of further reflection.

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Wei, Zuzhuang, Bobo Liu, Xiaomin Lin, Jing Wang, Zhi-Shu Huang, and Ding Li. "Development of a Smart Fluorescent Probe Specifically Interacting with C-Myc I-Motif." International Journal of Molecular Sciences 23, no. 7 (March 31, 2022): 3872. http://dx.doi.org/10.3390/ijms23073872.

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I-motifs play key regulatory roles in biological processes, holding great potential as attractive therapeutic targets. In the present study, we developed a novel fluorescent probe G59 with strong and selective binding to the c-myc gene promoter i-motif. G59 had an i-motif-binding carbazole moiety conjugated with naphthalimide fluorescent groups. G59 could differentiate the c-myc i-motif from other DNA structures through selective activation of its fluorescence, with its apparent visualization in solution. The smart probe G59 showed excellent sensitivity, with a low fluorescent detection limit of 154 nM and effective stabilization to the c-myc i-motif. G59 could serve as a rapid and sensitive probe for label-free screening of selective c-myc i-motif binding ligands under neutral crowding conditions. To the best of our knowledge, G59 is the first fluorescent probe with high sensitivity for recognizing the i-motif structure and screening for selective binding ligands.

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Gilbert, R., M. G. Kelly, T. Mikawa, and D. A. Fischman. "The carboxyl terminus of myosin binding protein C (MyBP-C, C-protein) specifies incorporation into the A-band of striated muscle." Journal of Cell Science 109, no. 1 (January 1, 1996): 101–11. http://dx.doi.org/10.1242/jcs.109.1.101.

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Myosin binding protein-C (MyBP-C), also known as C-protein, is a major constituent of the thick filaments of vertebrate striated muscles. The protein, approximately 130 kDa, consists of a series of 10 globular motifs (numbered I to X) each of approximately 90–100 amino acids, bearing resemblance to the C2-set of immunoglobins (Ig C2) and to the fibronectin type III (FnIII) motifs. Using pure preparations of myosin and MyBP-C, it has been demonstrated that the major myosin binding domain of MyBP-C resides within the C-terminal Ig C2 motif (motif X). However, in the context of the in vivo thick filament, it is uncertain if the latter domain is sufficient to target MyBP-C correctly to the A-band or if other regions of the molecule are required for this process. To answer this question, cultures of skeletal muscle myoblasts were transfected with expression plasmids encoding seven truncation mutants of MyBP-C, and their targeting to the A-band investigated by immunofluorescence microscopy. To distinguish the recombinant proteins from endogenous MyBP-C, a myc epitope was inserted at each amino terminus. Recombinant MyBP-C exhibited an identical distribution in the sarcomere to that of native MyBP-C; i.e. it was found exclusively in the C-zone of the A-band. A mutant encoding the C-terminal 372 amino acids, but lacking motifs I-VI (termed delta 1–6), also targeted correctly to the A-band. This fragment, which is composed of two Ig C2 and two FnIII motifs, was the minimal protein fragment required for correct A-band incorporation. Larger amino-terminal deletions or deletion of motif X, the myosin binding domain, abolished all localization to the A-band. One construct (delta 10) lacking only motif X strongly inhibited myofibril assembly. We conclude that the myosin binding domain of MyBP-C, although essential, is not sufficient for correct incorporation into the A-band and that motifs VII to IX are required for this process. The data suggest a topological model in which MyBP-C is associated with the thick filament through its C terminus.

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Journal articles on the topic 'I-Motifs'

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