Journal articles: 'Motifs du code circulaire'

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Michel, Christian J. "Circular code motifs in transfer RNAs." Computational Biology and Chemistry 45 (August 2013): 17–29. http://dx.doi.org/10.1016/j.compbiolchem.2013.02.004.

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El Soufi, Karim, and Christian J. Michel. "Circular code motifs in genomes of eukaryotes." Journal of Theoretical Biology 408 (November 2016): 198–212. http://dx.doi.org/10.1016/j.jtbi.2016.07.022.

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Fimmel, Elena, Christian J. Michel, and Lutz Strüngmann. "n -Nucleotide circular codes in graph theory." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, no. 2063 (March 13, 2016): 20150058. http://dx.doi.org/10.1098/rsta.2015.0058.

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The circular code theory proposes that genes are constituted of two trinucleotide codes: the classical genetic code with 61 trinucleotides for coding the 20 amino acids (except the three stop codons { TAA , TAG , TGA }) and a circular code based on 20 trinucleotides for retrieving, maintaining and synchronizing the reading frame. It relies on two main results: the identification of a maximal C 3 self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses (Michel 2015 J. Theor. Biol. 380, 156–177. ( doi:10.1016/j.jtbi.2015.04.009 ); Arquès & Michel 1996 J. Theor. Biol. 182, 45–58. ( doi:10.1006/jtbi.1996.0142 )) and the finding of X circular code motifs in tRNAs and rRNAs, in particular in the ribosome decoding centre (Michel 2012 Comput. Biol. Chem. 37, 24–37. ( doi:10.1016/j.compbiolchem.2011.10.002 ); El Soufi & Michel 2014 Comput. Biol. Chem. 52, 9–17. ( doi:10.1016/j.compbiolchem.2014.08.001 )). The univerally conserved nucleotides A1492 and A1493 and the conserved nucleotide G530 are included in X circular code motifs. Recently, dinucleotide circular codes were also investigated (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. ( doi:10.1155/2013/538631 ); Fimmel et al. 2015 J. Theor. Biol. 386, 159–165. ( doi:10.1016/j.jtbi.2015.08.034 )). As the genetic motifs of different lengths are ubiquitous in genes and genomes, we introduce a new approach based on graph theory to study in full generality n -nucleotide circular codes X , i.e. of length 2 (dinucleotide), 3 (trinucleotide), 4 (tetranucleotide), etc. Indeed, we prove that an n -nucleotide code X is circular if and only if the corresponding graph is acyclic. Moreover, the maximal length of a path in corresponds to the window of nucleotides in a sequence for detecting the correct reading frame. Finally, the graph theory of tournaments is applied to the study of dinucleotide circular codes. It has full equivalence between the combinatorics theory (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. ( doi:10.1155/2013/538631 )) and the group theory (Fimmel et al. 2015 J. Theor. Biol. 386, 159–165. ( doi:10.1016/j.jtbi.2015.08.034 )) of dinucleotide circular codes while its mathematical approach is simpler.

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El Soufi, Karim, and Christian J. Michel. "Unitary circular code motifs in genomes of eukaryotes." Biosystems 153-154 (March 2017): 45–62. http://dx.doi.org/10.1016/j.biosystems.2017.02.001.

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El Soufi, Karim, and Christian J. Michel. "Circular code motifs in the ribosome decoding center." Computational Biology and Chemistry 52 (October 2014): 9–17. http://dx.doi.org/10.1016/j.compbiolchem.2014.08.001.

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El Soufi, Karim, and Christian J. Michel. "Circular code motifs near the ribosome decoding center." Computational Biology and Chemistry 59 (December 2015): 158–76. http://dx.doi.org/10.1016/j.compbiolchem.2015.07.015.

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Blum, Christopher F., and Markus Kollmann. "Neural networks with circular filters enable data efficient inference of sequence motifs." Bioinformatics 35, no. 20 (March 27, 2019): 3937–43. http://dx.doi.org/10.1093/bioinformatics/btz194.

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Abstract Motivation Nucleic acids and proteins often have localized sequence motifs that enable highly specific interactions. Due to the biological relevance of sequence motifs, numerous inference methods have been developed. Recently, convolutional neural networks (CNNs) have achieved state of the art performance. These methods were able to learn transcription factor binding sites from ChIP-seq data, resulting in accurate predictions on test data. However, CNNs typically distribute learned motifs across multiple filters, making them difficult to interpret. Furthermore, networks trained on small datasets often do not generalize well to new sequences. Results Here we present circular filters, a novel convolutional architecture, that convolves sequences with circularly permutated variants of the same filter. We motivate circular filters by the observation that CNNs frequently learn filters that correspond to shifted and truncated variants of the true motif. Circular filters enable learning of full-length motifs and allow easy interpretation of the learned filters. We show that circular filters improve motif inference performance over a wide range of hyperparameters as well as sequence length. Furthermore, we show that CNNs with circular filters in most cases outperform conventional CNNs at inferring DNA binding sites from ChIP-seq data. Availability and implementation Code is available at https://github.com/christopherblum. Supplementary information Supplementary data are available at Bioinformatics online.

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Michel, Christian J. "Single-Frame, Multiple-Frame and Framing Motifs in Genes." Life 9, no. 1 (February 10, 2019): 18. http://dx.doi.org/10.3390/life9010018.

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We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is SF as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame SF is multiple-frame MF. Several classes of MF motifs are defined and analysed. The distributions of single-frame SF motifs (associated with an unambiguous trinucleotide decoding in the two 5'–3' and 3'–5' directions) and 5′ unambiguous motifs 5'U (associated with an unambiguous trinucleotide decoding in the 5'–3' direction only) are analysed without and with constraints. The constraints studied are: initiation and stop codons, periodic codons AAA,CCC,GGG,TTT, antiparallel complementarity and parallel complementarity. Taken together, these results suggest that the complementarity property involved in the antiparallel (DNA double helix, RNA stem) and parallel sequences could also be fundamental for coding genes with an unambiguous trinucleotide decoding in the two 5'–3' and 3'–5' directions or the 5'–3' direction only. Furthermore, the single-frame motifs SF with a property of trinucleotide decoding and the framing motifs F (also called circular code motifs; first introduced by Michel (2012)) with a property of reading frame decoding may have been involved in the early life genes to build the modern genetic code and the extant genes. They could have been involved in the stage without anticodon-amino acid interactions or in the Implicated Site Nucleotides (ISN) of RNA interacting with the amino acids. Finally, the SF and MF dipeptides associated with the SF and MF dicodons, respectively, are studied and their importance for biology and the origin of life discussed.

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Wang, Jun, and Liangjiang Wang. "Deep learning of the back-splicing code for circular RNA formation." Bioinformatics 35, no. 24 (May 11, 2019): 5235–42. http://dx.doi.org/10.1093/bioinformatics/btz382.

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Abstract Motivation Circular RNAs (circRNAs) are a new class of endogenous RNAs in animals and plants. During pre-RNA splicing, the 5′ and 3′ termini of exon(s) can be covalently ligated to form circRNAs through back-splicing (head-to-tail splicing). CircRNAs can be conserved across species, show tissue- and developmental stage-specific expression patterns, and may be associated with human disease. However, the mechanism of circRNA formation is still unclear although some sequence features have been shown to affect back-splicing. Results In this study, by applying the state-of-art machine learning techniques, we have developed the first deep learning model, DeepCirCode, to predict back-splicing for human circRNA formation. DeepCirCode utilizes a convolutional neural network (CNN) with nucleotide sequence as the input, and shows superior performance over conventional machine learning algorithms such as support vector machine and random forest. Relevant features learnt by DeepCirCode are represented as sequence motifs, some of which match human known motifs involved in RNA splicing, transcription or translation. Analysis of these motifs shows that their distribution in RNA sequences can be important for back-splicing. Moreover, some of the human motifs appear to be conserved in mouse and fruit fly. The findings provide new insight into the back-splicing code for circRNA formation. Availability and implementation All the datasets and source code for model construction are available at https://github.com/BioDataLearning/DeepCirCode. Supplementary information Supplementary data are available at Bioinformatics online.

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Michel, Christian J. "Circular code motifs in transfer and 16S ribosomal RNAs: A possible translation code in genes." Computational Biology and Chemistry 37 (April 2012): 24–37. http://dx.doi.org/10.1016/j.compbiolchem.2011.10.002.

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Dila, Gopal, Christian J. Michel, Olivier Poch, Raymond Ripp, and Julie D. Thompson. "Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes." Biosystems 175 (January 2019): 57–74. http://dx.doi.org/10.1016/j.biosystems.2018.10.014.

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Dila, Gopal, Raymond Ripp, Claudine Mayer, Olivier Poch, Christian J. Michel, and Julie D. Thompson. "Circular code motifs in the ribosome: a missing link in the evolution of translation?" RNA 25, no. 12 (September 10, 2019): 1714–30. http://dx.doi.org/10.1261/rna.072074.119.

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Improta, Roberto. "Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations." International Journal of Molecular Sciences 24, no. 16 (August 9, 2023): 12614. http://dx.doi.org/10.3390/ijms241612614.

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I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical–physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.

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Ohmaid, Hicham, S. Eddarouich, A. Bourouhou, and M. Timouya. "Comparison between SVM and KNN classifiers for iris recognition using a new unsupervised neural approach in segmentation." IAES International Journal of Artificial Intelligence (IJ-AI) 9, no. 3 (September 1, 2020): 429. http://dx.doi.org/10.11591/ijai.v9.i3.pp429-438.

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Un système biométrique d'identification et d'authentification permet la reconnaissance automatique d'un individu en fonction de certaines caractéristiques ou caractéristiques uniques qu'il possède. La reconnaissance de l'iris est une méthode d'identification biométrique qui applique la reconnaissance des formes aux images de l'iris. En raison des motifs épigénétiques uniques de l'iris, la reconnaissance de l'iris est considérée comme l'une des méthodes les plus précises dans le domaine de l'identification biométrique. L'algorithme de segmentation proposé dans cet article commence par déterminer les régions de l'œil à l'aide d'une approche neuronale non supervisée, après que le contour de l'œil a été trouvé à l'aide du bord de Canny, la transformation de Hough est utilisée pour déterminer le centre et le rayon de la pupille et de l'iris. . Ensuite, la normalisation permet de transformer la région de l'iris circulaire segmenté en une forme rectangulaire de taille fixe en utilisant le modèle de feuille de caoutchouc de Daugman. Une transformation en ondelettes discrètes (DWT) est appliquée à l'iris normalisé pour réduire la taille des modèles d'iris et améliorer la précision du classificateur. Enfin, la base de données URIBIS iris est utilisée pour la vérification individuelle de l'utilisateur en utilisant le classificateur KNN ou la machine à vecteur de support (SVM) qui, sur la base de l'analyse du code de l'iris lors de l'extraction des caractéristiques, est discutée.

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Gellatly, Duncan, Kayvan Mirhadi, Srividhya Venkataraman, and Mounir G. AbouHaidar. "Structural and sequence integrity are essential for the replication of the viroid-like satellite RNA of lucerne transient streak virus." Journal of General Virology 92, no. 6 (June 1, 2011): 1475–81. http://dx.doi.org/10.1099/vir.0.029801-0.

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Lucerne transient streak virus (LTSV, genus Sobemovirus) supports the replication and encapsidation of a 322 nt untranslated small-circular RNA (scLTSV). Since scLTSV does not code for any proteins or share sequence similarity with its helper virus (LTSV), it is presumed that it uses structural and sequence motifs to signal the helper virus (and host) machinery for its replication and encapsidation. Insertion and deletion mutations were introduced at various locations within the scLTSV molecule. Our results showed that most mutants were not infectious, with only two exceptions, a (−1) nucleotide deletion and a 9 nt, palindromic insertion mutant which preserved the overall rod-like structure of the scLTSV. Sequence analysis of cDNA clones revealed that the palindromic sequence was replicated for up to 12 days of infection, before the sequence reverted back to its wild-type form. Our results indicate that scLTSV has an optimal sequence and secondary structure for replication, movement and/or packaging within the LTSV helper virus.

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Gainor, Kerry, Yashpal S. Malik, and Souvik Ghosh. "Novel Cyclovirus Species in Dogs with Hemorrhagic Gastroenteritis." Viruses 13, no. 11 (October 26, 2021): 2155. http://dx.doi.org/10.3390/v13112155.

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Nested PCRs with circovirus/cyclovirus pan-rep (replicase gene) primers detected eukaryotic circular Rep-encoding single-stranded DNA (CRESS DNA) viruses in three (samples CN9E, CN16E and CN34) of 18 canine parvovirus-2-positive fecal samples from household dogs with hemorrhagic gastroenteritis on the Caribbean island of Nevis. The complete genomes of CRESS DNA virus CN9E, CN16E and CN34 were determined by inverse nested PCRs. Based on (i) genome organization, (ii) location of the putative origin of replication, (iii) pairwise genome-wide sequence identities, (iv) the presence of conserved motifs in the putative replication-associated protein (Rep) and the arginine-rich region in the amino terminus of the putative capsid protein (Cp) and (v) a phylogenetic analysis, CN9E, CN16E and CN34 were classified as cycloviruses. Canine-associated cycloviruses CN16E and CN34 were closely related to each other and shared low genome-wide nucleotide (59.642–59.704%), deduced Rep (35.018–35.379%) and Cp (26.601%) amino acid sequence identities with CN9E. All the three canine-associated cycloviruses shared < 80% genome-wide pairwise nucleotide sequence identities with cycloviruses from other animals/environmental samples, constituting two novel species (CN9E and CN16E/34) within the genus Cyclovirus. Considering the feeding habits of dogs, we could not determine whether the cycloviruses were of dietary origin or infected the host. Interestingly, the CN9E putative Rep-encoding open reading frame was found to use the invertebrate mitochondrial genetic code with an alternative initiation codon (ATA) for translation, corroborating the hypothesis that cycloviruses are actually arthropod-infecting viruses. To our knowledge, this is the first report on the detection and complete genome analysis of cycloviruses from domestic dogs.

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Gumbel, M., and P. Wiedemann. "Motif lengths of circular codes in coding sequences." Journal of Theoretical Biology 523 (August 2021): 110708. http://dx.doi.org/10.1016/j.jtbi.2021.110708.

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de la Cruz, Xavier, Sergio Lois, Sara Sánchez-Molina, and Marian A. Martínez-Balbás. "Do protein motifs read the histone code?" BioEssays 27, no. 2 (January 21, 2005): 164–75. http://dx.doi.org/10.1002/bies.20176.

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Devoet, Claude. "L’article 8 du Code des droits de succession selon la vision nouvelle de l’administration fiscale fédérale." Forum de l’assurance N° 213, no. 4 (April 1, 2021): 69–77. http://dx.doi.org/10.3917/foas.213.0069.

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L’administration fédérale a revu sa position par sa circulaire 2021/C/2 du 7 janvier 2021 relative à l’article 8 du Code des droits de succession et à la taxation applicable selon divers types de contrat d’assurance vie. Elle distille ses « commentaires administratifs relatifs à l’article 8 du Code des droits de succession et à la taxation à opérer en fonction de la structure du contrat d’assurance vie concernant un défunt, ce dernier pouvant y intervenir à titre de preneur et/ou assuré et/ou bénéficiaire, tant dans les cas où le défunt est un conjoint marié sous un régime de communauté que dans les cas où le défunt n’est pas marié ou marié sous un régime de séparation de biens ».

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Roca-Martínez, Joel, Hrishikesh Dhondge, Michael Sattler, and Wim F. Vranken. "Deciphering the RRM-RNA recognition code: A computational analysis." PLOS Computational Biology 19, no. 1 (January 23, 2023): e1010859. http://dx.doi.org/10.1371/journal.pcbi.1010859.

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RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eukaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA recognition code has remained elusive. An increasing number of experimental structures of RRM-RNA complexes has become available in recent years. Here, we perform an in-depth computational analysis to derive an RNA recognition code for canonical RRMs. We present and validate a computational scoring method to estimate the binding between an RRM and a single stranded RNA, based on structural data from a carefully curated multiple sequence alignment, which can predict RRM binding RNA sequence motifs based on the RRM protein sequence. Given the importance and prevalence of RRMs in humans and other species, this tool could help design RNA binding motifs with uses in medical or synthetic biology applications, leading towards the de novo design of RRMs with specific RNA recognition.

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Grabowski, P. J. "A molecular code for splicing silencing: configurations of guanosine-rich motifs." Biochemical Society Transactions 32, no. 6 (October 26, 2004): 924–27. http://dx.doi.org/10.1042/bst0320924.

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Alternative pre-mRNA splicing is frequently used to expand the protein-coding capacity of genomes, and to regulate gene expression at the post-transcriptional level. It is a significant challenge to decipher the molecular language of tissue-specific splicing because the inherent flexibility of these mechanisms is specified by numerous short sequence motifs distributed in introns and exons. In the present study, we employ the glutamate NMDA (N-methyl-D-aspartate) R1 receptor (GRIN1) transcript as a model system to identify the molecular determinants for a brain region-specific exon silencing mechanism. We identify a set of guanosine-rich motifs that function co-operatively to regulate the CI cassette exon in a manner consistent with its in vivo splicing pattern. Whereas hnRNP (heterogeneous nuclear ribonucleoprotein) A1 mediates silencing of the CI cassette exon in conjunction with the guanosine-rich motifs, hnRNP H functions as an antagonist to silencing. Genome-wide analysis shows that, while this motif pattern is rarely present in human and mouse exons, those exons for which the pattern is conserved are generally found to be skipped exons. The identification of a similar arrangement of guanosine-rich motifs in transcripts of the hnRNP H family of splicing factors has implications for their co-ordinate regulation at the level of splicing.

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LEGENDRE, Camille. "Note de recherche — Le refus de retrait préventif de la travailleuse enceinte ou qui allaite : résultats préliminaires." Sociologie et sociétés 18, no. 2 (September 30, 2002): 129–36. http://dx.doi.org/10.7202/001424ar.

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Résumé À la suite d'une étude des dossiers de demandes de retrait préventif par les travailleuses enceintes ou qui allaitent, l'auteur examine le recours à cette mesure novatrice de prévention à la lumière des demandes refusées par la Commission de la santé et de la sécurité au travail (CSST). Il considère tour à tour les principales caractéristiques des demandes refusées et les motifs de ces refus. L'analyse montre que la proportion de refus varie selon plusieurs facteurs (l'occupation, le secteur d'activité économique et la région). L'étude montre que le nombre de refus est plus élevé que ne l'indiquent les statistiques officielles et que le code des motifs de refus utilisé par la CSST rend très mal compte des véritables motifs invoqués et devrait être remplacé par un code spécifique à ce programme de santé et de sécurité au travail.

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Shao, Ping, Yang Yang, Shengyao Xu, and Chunping Wang. "Network Embedding via Motifs." ACM Transactions on Knowledge Discovery from Data 16, no. 3 (June 30, 2022): 1–20. http://dx.doi.org/10.1145/3473911.

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Network embedding has emerged as an effective way to deal with downstream tasks, such as node classification [ 16 , 31 , 42 ]. Most existing methods leverage multi-similarities between nodes such as connectivity, which considers vertices that are closely connected to be similar and structural similarity, which is measured by assessing their relations to neighbors; while these methods only focus on static graphs. In this work, we bridge connectivity and structural similarity in a uniform representation via motifs, and consequently present an algorithm for Learning Embeddings by leveraging Motifs Of Networks (LEMON), which aims to learn embeddings for vertices and various motifs. Moreover, LEMON is inherently capable of dealing with inductive learning tasks for dynamic graphs. To validate the effectiveness and efficiency, we conduct various experiments on two real-world datasets and five public datasets from diverse domains. Through comparison with state-of-the-art baseline models, we find that LEMON achieves significant improvements in downstream tasks. We release our code on Github at https://github.com/larry2020626/LEMON.

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Li, Yang, Pengyu Ni, Shaoqiang Zhang, Guojun Li, and Zhengchang Su. "ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery." Bioinformatics 35, no. 22 (May 9, 2019): 4632–39. http://dx.doi.org/10.1093/bioinformatics/btz290.

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Abstract Motivation The availability of numerous ChIP-seq datasets for transcription factors (TF) has provided an unprecedented opportunity to identify all TF binding sites in genomes. However, the progress has been hindered by the lack of a highly efficient and accurate tool to find not only the target motifs, but also cooperative motifs in very big datasets. Results We herein present an ultrafast and accurate motif-finding algorithm, ProSampler, based on a novel numeration method and Gibbs sampler. ProSampler runs orders of magnitude faster than the fastest existing tools while often more accurately identifying motifs of both the target TFs and cooperators. Thus, ProSampler can greatly facilitate the efforts to identify the entire cis-regulatory code in genomes. Availability and implementation Source code and binaries are freely available for download at https://github.com/zhengchangsulab/prosampler. It was implemented in C++ and supported on Linux, macOS and MS Windows platforms. Supplementary information Supplementary materials are available at Bioinformatics online.

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Han, Kyoungha, Gene Yeo, Ping An, Christopher B. Burge, and Paula J. Grabowski. "A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs." PLoS Biology 3, no. 5 (April 19, 2005): e158. http://dx.doi.org/10.1371/journal.pbio.0030158.

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Cheng, Alice, Charles E. Grant, William S. Noble, and Timothy L. Bailey. "MoMo: discovery of statistically significant post-translational modification motifs." Bioinformatics 35, no. 16 (December 31, 2018): 2774–82. http://dx.doi.org/10.1093/bioinformatics/bty1058.

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Abstract Motivation Post-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called ‘motifs’ that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. Accurate statistical confidence estimates for discovered motifs are critically important for proper interpretation and in the design of downstream experimental validation. Results We describe a method for assigning statistical confidence estimates to PTM motifs, and we demonstrate that this method provides accurate P-values on both simulated and real data. Our methods are implemented in MoMo, a software tool for discovering motifs among sets of PTMs that we make available as a web server and as downloadable source code. MoMo re-implements the two most widely used PTM motif discovery algorithms—motif-x and MoDL—while offering many enhancements. Relative to motif-x, MoMo offers improved statistical confidence estimates and more accurate calculation of motif scores. The MoMo web server offers more proteome databases, more input formats, larger inputs and longer running times than the motif-x web server. Finally, our study demonstrates that the confidence estimates produced by motif-x are inaccurate. This inaccuracy stems in part from the common practice of drawing ‘background’ peptides from an unshuffled proteome database. Our results thus suggest that many of the papers that use motif-x to find motifs may be reporting results that lack statistical support. Availability and implementation The MoMo web server and source code are provided at http://meme-suite.org. Supplementary information Supplementary data are available at Bioinformatics online.

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Raykhel, Irina, Heli Alanen, Kirsi Salo, Jaana Jurvansuu, Van Dat Nguyen, Maria Latva-Ranta, and Lloyd Ruddock. "A molecular specificity code for the three mammalian KDEL receptors." Journal of Cell Biology 179, no. 6 (December 17, 2007): 1193–204. http://dx.doi.org/10.1083/jcb.200705180.

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AC-terminal KDEL-like motif prevents secretion of soluble endoplasmic reticulum (ER)–resident proteins. This motif interacts with KDEL receptors localized in the intermediate compartment and Golgi apparatus. Such binding triggers retrieval back to the ER via a coat protein I–dependent pathway. To date, two human KDEL receptors have been reported. Here, we report the Golgi localization of a third human KDEL receptor. Using a reporter construct system from a screen of 152 variants, we identified 35 KDEL-like variants that result in efficient ER localization but do not match the current Prosite motif for ER localization ([KRHQSA]-[DENQ]-E-L). We cloned 16 human proteins with one of these motifs and all were found in the ER. A subsequent screen by bimolecular fluorescence complementation determined the specificities of the three human KDEL receptors. Each KDEL receptor has a unique pattern of motifs with which it interacts. This suggests a specificity in the retrieval of human proteins that contain different KDEL variants.

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ARKIN, HANDAN, FATİH YAŞAR, TARIK ÇELİK, SÜEDA ÇELİK, and HAMİT KÖKSEL. "MOLECULAR MODELING OF TWO HEXAPEPTIDE REPEAT MOTIFS OF HMW GLUTENIN SUBUNITS." International Journal of Modern Physics C 12, no. 02 (February 2001): 281–92. http://dx.doi.org/10.1142/s0129183101001675.

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The three-dimensional structures of two hexapeptide repeat motifs (PGQGQQ and SGQGQQ, in one letter code) in the repetitive central domain of HMW glutenin subunits are investigated by using the multicanonical simulation procedure. Ramachandran plots were prepared and analyzed to predict the relative occurrence probabilities of β-turn and γ-turn structures and helical state. Structural predictions of PGQGQQ repeat motif indicated the presence of high level of β-turns and considerable level of γ-turns. Simulations of the repeat motifs in the repetitive central domain of HMW glutenin subunits indicated that these structures take important part in the three-dimensional structures of repeat motifs.

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Al-Khafaji, Hussein, and Ghada Kassim. "A New Approach to Motif Templates Analysis via Compilation Technique." Journal of Al-Rafidain University College For Sciences ( Print ISSN: 1681-6870 ,Online ISSN: 2790-2293 ), no. 2 (October 15, 2021): 180–208. http://dx.doi.org/10.55562/jrucs.v34i2.289.

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Motif template assertion and analysis is compulsory operation in most of bioinformatics systems such as motif search, sequential pattern miner, and bioinformatics databases analysis. The motif template can be in any length, therefore, the typing errors increased according to the length of motif. Also, when the structure motifs are submitted to bioinformatics systems they require specification of their components, i.e. the simple motifs, gaps, and the limits of the gaps. This research proposed a context free grammar, GFC, to describe the motif structure, and then this CFG is utilized to design an interpreter to detect, debug the errors, and analyze the motif template to its components. All the errors of 100 motifs of length arranged from 100 Base to 10 KBase are detected. These motifs are entered by 10 data entries. The experiments showed high correlation between number of errors and number of gaps, size of simple motifs, and motif template size. The target code of the interpreter is the components of a submitted motif template to be used in bioinformatics systems as next steps

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Ramos, Fernanda Ledo G., Fernando P. De Miranda, Alexandre G. Evsukoff, Emmanuel Trouvé, and Sylvie Galichet. "Fusion d'informations issues de la télédétection radar pour l'observation de déplacements dans la région de Manaus (Amazonie)." Revue Française de Photogrammétrie et de Télédétection, no. 198-199 (April 21, 2014): 30–38. http://dx.doi.org/10.52638/rfpt.2012.69.

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En mesurant la différence de phase entre des images acquises dans les mêmes conditions à des dates différentes, l’interférométrie radar différentielle (DInSAR) permet d’observer des déplacements de la surface avec une précision de l’ordre de la longueur d’onde : quelques centimètres en bande C. Dans cet article, l´interférométrie appliquée à une série de 15 images Radarsat-1 et 24 images Radarsat 2 acquises entre 2006 et 2010 a permis d´étudier les phénomènes géophysiques liés aux déformations de terrain dans la ville de Manaus, la plus grande de l´Amazonie, au Brésil. Nous nous plaçons dans ce cadre pour analyser le contexte tectonique et structural des résultats obtenus par cette étude.Cette approche inclut l´analyse du réseau de drainage extrait du modèle numérique de terrain SRTM (Shuttle Radar Mission Topography) ainsi que la comparaison de différentes images satellitaires optiques avec des informations géologiques et géomorphologiques existantes. Les résultats montrent l´existence probable de déplacements dans une région à coté d´une anomalie circulaire de drainage (4 km de diamètre). La combinaison de l’ensemble des données disponibles fournit une interprétation géologique aux différents motifs obtenus par l´étude interférométrique.

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Oliver, Carlos, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, and Jérôme Waldispühl. "Vernal: a tool for mining fuzzy network motifs in RNA." Bioinformatics 38, no. 4 (November 15, 2021): 970–76. http://dx.doi.org/10.1093/bioinformatics/btab768.

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Abstract Motivation RNA 3D motifs are recurrent substructures, modeled as networks of base pair interactions, which are crucial for understanding structure–function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State-of-the-art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space. Results Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods and motif construction algorithms to recover flexible RNA motifs. Our tool, Vernal can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that Vernal is able to retrieve and expand known classes of motifs, as well as to propose novel motifs. Availability and implementation The source code, data and a webserver are available at vernal.cs.mcgill.ca. We also provide a flexible interface and a user-friendly webserver to browse and download our results. Supplementary information Supplementary data are available at Bioinformatics online.

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Schlusser, Niels, and Mihaela Zavolan. "On the limits of inferring biophysical parameters of RBP-RNA interactions from in vitro RNA Bind’n Seq data." F1000Research 12 (June 26, 2023): 742. http://dx.doi.org/10.12688/f1000research.135164.1.

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We develop a thermodynamic model describing the binding of RNA binding proteins (RBP) to oligomers in vitro. We apply expectation-maximization to infer the specificity of RBPs, represented as position-specific weight matrices (PWMs), by maximizing the likelihood of RNA Bind’n Seq data from the ENCODE project. We demonstrate that the model can reproduce known specificities for well-studied proteins and that in some cases we predict novel, longer binding motifs. However, the model does not recover all the motifs that are in principle known, indicating that the data is not well explained by a single underlying biophysical model. Our code is publicly available.

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Sun, Saisai, Jianyi Yang, and Zhaolei Zhang. "RNALigands: a database and web server for RNA–ligand interactions." RNA 28, no. 2 (November 3, 2021): 115–22. http://dx.doi.org/10.1261/rna.078889.121.

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RNA molecules can fold into complex and stable 3D structures, allowing them to carry out important genetic, structural, and regulatory roles inside the cell. These complex structures often contain 3D pockets made up of secondary structural motifs that can be potentially targeted by small molecule ligands. Indeed, many RNA structures in PDB contain bound small molecules, and high-throughput experimental studies have generated a large number of interacting RNA and ligand pairs. There is considerable interest in developing small molecule lead compounds targeting viral RNAs or those RNAs implicated in neurological diseases or cancer. We hypothesize that RNAs that have similar secondary structural motifs may bind to similar small molecule ligands. Toward this goal, we established a database collecting RNA secondary structural motifs and bound small molecule ligands. We further developed a computational pipeline, which takes as input an RNA sequence, predicts its secondary structure, extracts structural motifs, and searches the database for similar secondary structure motifs and interacting small molecule. We demonstrated the utility of the server by querying α-synuclein mRNA 5′ UTR sequence and finding potential matches which were validated as correct. The server is publicly available at http://RNALigands.ccbr.utoronto.ca. The source code can also be downloaded at https://github.com/SaisaiSun/RNALigands.

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Muslimov, Ilham A., Mihir V. Patel, Arthur Rose, and Henri Tiedge. "Spatial code recognition in neuronal RNA targeting: Role of RNA–hnRNP A2 interactions." Journal of Cell Biology 194, no. 3 (August 1, 2011): 441–57. http://dx.doi.org/10.1083/jcb.201010027.

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In neurons, regulation of gene expression occurs in part through translational control at the synapse. A fundamental requirement for such local control is the targeted delivery of select neuronal mRNAs and regulatory RNAs to distal dendritic sites. The nature of spatial RNA destination codes, and the mechanism by which they are interpreted for dendritic delivery, remain poorly understood. We find here that in a key dendritic RNA transport pathway (exemplified by BC1 RNA, a dendritic regulatory RNA, and protein kinase M ζ [PKMζ] mRNA, a dendritic mRNA), noncanonical purine•purine nucleotide interactions are functional determinants of RNA targeting motifs. These motifs are specifically recognized by heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2), a trans-acting factor required for dendritic delivery. Binding to hnRNP A2 and ensuing dendritic delivery are effectively competed by RNAs with CGG triplet repeat expansions. CGG repeats, when expanded in the 5′ untranslated region of fragile X mental retardation 1 (FMR1) mRNA, cause fragile X–associated tremor/ataxia syndrome. The data suggest that cellular dysregulation observed in the presence of CGG repeat RNA may result from molecular competition in neuronal RNA transport pathways.

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Marleau, Véronique L. "Décision rendue par le Conseil canadien des relations du travail." Discussion 45, no. 2 (April 12, 2005): 414–23. http://dx.doi.org/10.7202/050590ar.

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Saisi de la question de savoir si une personne opérant un comptoir postal était un employé au sens du Code canadien du travail (le Code), le Conseil a examiné de façon différente le test applicable en matière de détermination du statut d'entrepreneur indépendant. Dans ses motifs, le Conseil note qu'en adoptant la définition d'entrepreneur indépendant retrouvée au paragraphe 3(1) du Code, le Parlement a privilégié la notion de dépendance économique comme élément distinctif des statuts d'entrepreneur dépendant et indépendant. Par conséquent, le Conseil, soucieux d'appliquer un test à même de refléter plus fidèlement l'importance attribuée à cet élément-clé, applique de nouveaux critères reliés au contrôle économique tout en mettant l'emphase sur les activités de l'entrepreneur plutôt que sur l'entreprise de l'employeur.

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Panina, Tatiana Igorevna. "Semantic Models and Motifs of the Actional Code of the Udmurt Healing Ritual." Manuskript, no. 12 (December 2021): 2597–602. http://dx.doi.org/10.30853/mns20210465.

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KUMAR, Sudheer, Deepak MAURYA, Shalini RAI, Prem Lal KASHYAP, and Alok Kumar SRIVASTAVA. "Computational Mining and Genome Wide Distribution of Microsatellite in Fusarium oxysporum f. sp. lycopersici." Notulae Scientia Biologicae 4, no. 4 (November 6, 2012): 127–31. http://dx.doi.org/10.15835/nsb448271.

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Simple sequence repeat (SSR) is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Hence, in present study an attempt was made to mine and analyze microsatellite dynamics in whole genome of Fusarium oxysporum f. sp. lycopersici. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of tetra-nucleotide (3837) repeats followed by tri-nucleotide (3367) repeats. Maximum frequency distribution in coding region was shown by mono-nucleotide SSR motifs (34.8%), where as minimum frequency is observed for penta-nucleotide SSR (0.87%). Highest relative abundance (1023 SSR/Mb) and density of SSRs (114.46 bp/Mb) were observed on chromosome 1, while least density of SSR motifs was recorded on chromosome 11 (7.40 bp/Mb) and 12 (7.41 bp/Mb), respectively. Maximum trinucleotide (34.24%) motifs code for glutamic acid (GAA) while GT/CT were the most frequent repeat of dinucleotide SSRs. Most common and highly repeated SSR motifs were identified as (A)64, (T)48, (GT)24, (GAA)31, (TTTC)24, (TTTCT)28 and (AACCAG)27. Overall, the generated information may serve as baseline information for developing SSR markers that could find applications in genomic analysis of F. oxysporum f. sp. lycopersici for better understanding of evolution, diversity analysis, population genetics, race identification and acquisition of new virulence.

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Löchel, Hannah F., Marius Welzel, Georges Hattab, Anne-Christin Hauschild, and Dominik Heider. "Fractal construction of constrained code words for DNA storage systems." Nucleic Acids Research 50, no. 5 (December 15, 2021): e30-e30. http://dx.doi.org/10.1093/nar/gkab1209.

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Abstract The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. One is to use DNA as a storage medium, and the other is to use DNA for computing. Both strategies come with certain constraints. In the current study, we present a novel approach derived from chaos game representation for DNA to generate DNA code words that fulfill user-defined constraints, namely GC content, homopolymers, and undesired motifs, and thus, can be used to build codes for reliable DNA storage systems.

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Wong, Emily S., Dawei Zheng, Siew Z. Tan, Neil I. Bower, Victoria Garside, Gilles Vanwalleghem, Federico Gaiti, et al. "Deep conservation of the enhancer regulatory code in animals." Science 370, no. 6517 (November 5, 2020): eaax8137. http://dx.doi.org/10.1126/science.aax8137.

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Interactions of transcription factors (TFs) with DNA regulatory sequences, known as enhancers, specify cell identity during animal development. Unlike TFs, the origin and evolution of enhancers has been difficult to trace. We drove zebrafish and mouse developmental transcription using enhancers from an evolutionarily distant marine sponge. Some of these sponge enhancers are located in highly conserved microsyntenic regions, including an Islet enhancer in the Islet-Scaper region. We found that Islet enhancers in humans and mice share a suite of TF binding motifs with sponges, and that they drive gene expression patterns similar to those of sponge and endogenous Islet enhancers in zebrafish. Our results suggest the existence of an ancient and conserved, yet flexible, genomic regulatory syntax that has been repeatedly co-opted into cell type–specific gene regulatory networks across the animal kingdom.

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Ganin, Maxim V. "“Singing mountains” in the late Khlebnikov’s poetic manner: geognostic code in the autocommunicative model." RUDN Journal of Studies in Literature and Journalism 25, no. 2 (December 15, 2020): 214–25. http://dx.doi.org/10.22363/2312-9220-2020-25-2-214-225.

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This article analyzes the peculiarities of realization of the motif of singing mountains (and its variations) in the later period of artistic and philosophical searches of Russian poet and thinker, one of the originators of futuristic movement - Velimir Khlebnikov. Representations of the geognostic code are given in the paradigm of autocommunicative model peculiar to philosophical and aesthetic thinking of the poet. The actuality of the work is determined by the insufficient previous study of the problem of functioning of geognostic elements in the Khlebnikovs universe, as well as the importance of studying the autocommunicative strategies implemented in poetic texts with a complex structure and a high degree of encryption of the material. Structural semiotic and mythopoetic approaches together with elements of textological and componential analysis methods allowed to reveal mythopoetic motifs that are structurally and typologically close to the phenomenon of singing mountains. Based on the consideration of the post-revolutionary works of rechetvorets (wordwright) an assumption is made that their geognostic motifs can be configured both at the level of mythopoetic units and additional codes, and of natural objects that become independent communicators (addressant and addressee) in the system I - I. The contours of intertextual field analysis in the space of implementation of the considered motif are outlined.

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Alcántara-Silva, Rogelio, Moisés Alvarado-Hermida, Gibrán Díaz-Contreras, Martha Sánchez-Barrios, Samantha Carrera, and Silvia Carolina Galván. "PISMA: A Visual Representation of Motif Distribution in DNA Sequences." Bioinformatics and Biology Insights 11 (January 1, 2017): 117793221770090. http://dx.doi.org/10.1177/1177932217700907.

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Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

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Miller, Ira, Georgia Hatzivassiliou, Giorgio Cattoretti, Cathy Mendelsohn, and Riccardo Dalla-Favera. "IRTAs: a new family of immunoglobulinlike receptors differentially expressed in B cells." Blood 99, no. 8 (April 15, 2002): 2662–69. http://dx.doi.org/10.1182/blood.v99.8.2662.

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Abstract The IRTA1 and IRTA2 genes encode immunoglobulinlike cell surface receptors expressed in B cells and involved in chromosome 1q21 translocations in B-cell malignancy. We have now characterized and comparatively analyzed the structure and expression pattern of the entire family of IRTA genes, which includes 5 members contiguously located on chromosome 1q21. The IRTA messenger RNAs are expressed predominantly in the B-cell lineage within discrete B-cell compartments: IRTA1 is specific to the marginal zone, IRTA2 and IRTA3 are found in the germinal center light zone and in intraepithelial and interfollicular regions, and IRTA4 and IRTA5 are expressed predominantly in the mantle zone. All IRTA genes code for transmembrane receptors that are closely related to Fc receptors in their most amino-terminal extracellular domains and that possess cytoplasmic domains containing ITIM (immunotyrosine inhibition motifs)– and, possibly, ITAM (immunotyrosine activation motifs)–like motifs. These structural features suggest that the IRTA receptors may play a role in regulating activation of normal B cells and possibly in the development of neoplasia.

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Kluczyk, Alicja, Marek Cebrat, Renata Zbozień-Pacamaj, Marek Lisowski, Piotr Stefanowicz, Zbigniew Wieczorek, and Ignacy Z. Siemion. "On the peptide-antipeptide interactions in interleukin-1 receptor system." Acta Biochimica Polonica 51, no. 1 (March 31, 2004): 57–66. http://dx.doi.org/10.18388/abp.2004_3596.

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Interleukin-1 receptor antagonist (IL-1Ra) and vaccinia virus protein C10L share a VTXFYF motif, with X being Lys or Arg residue, respectively. Peptides of such sequence compete successfully with IL-1 for the cellular receptor. A pair of complementary peptides, based on the Siemion's hypothesis on the periodicity of the genetic code (QWLNIN and QWANIN), and another pair, in which, following the Root- Bernstein theory, Lys was used as complementary amino acid to Phe (QWLKIK and QWAKIK), were investigated for the peptide-antipeptide interactions using mass spectrometry (ESI-MS) and circular dichroism (CD) methods. The CD measurements indicated some conformational changes, more pronounced in the Siemion's pairs, however, no heterodimer formation was found by MS. In the region of IL-1 receptor situated close to the position of IL-1Ra in the IL-1Ra-receptor complex, a KQKL motif is present, suggesting a possibility of complementary recognition of the Root-Bernstein type in the IL-1 receptor. The biological activity of the complementary peptides is similar to that of the original ones. They efficiently compete with IL-1 and show moderate immunosuppressory activity in humoral and cellular immune response. The inhibition of the IL-1-IL-1 receptor interaction may result from the complementary peptides acting as mini-receptors with affinity for IL-1.

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Chirac, Jacques, and Albin Chalandon. "Projet de loi portant réforme du code de la nationalité française. Exposé des motifs." Hommes et Migrations 1099, no. 1 (1987): 22–27. http://dx.doi.org/10.3406/homig.1987.1030.

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Zhao, Dongxin, and Zhongxian Huang. "Recognition Code of ZNF191(243-368) and Its Interaction with DNA." Bioinorganic Chemistry and Applications 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/416751.

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ZNF191(243-368) is the C-terminal region of ZNF191 which contains a putative DNA-binding domain of four Cys2His2zinc finger motifs. In this study, an expression vector of a fusion protein of ZNF191(243-368) with glutathione-S-transferase (GST) was constructed and transformed intoEscherichia coliBL21. The fusion protein GST-ZNF191(243-368) was expressed using this vector to investigate the protein-DNA binding reaction through an affinity selection strategy on the basis of the binding quality of the zinc finger domain. Results showed that ZNF191(243-368) can selectively bind with sequences and react with genes which contain an AGGG core. However, the recognition mechanism of Cys2His2zinc finger proteins to DNA warrants further investigation.

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Santos, João D., Sara Canato, Ana S. Carvalho, Hugo M. Botelho, Kerman Aloria, Margarida D. Amaral, Rune Matthiesen, Andre O. Falcao, and Carlos M. Farinha. "Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum." Cells 8, no. 4 (April 14, 2019): 353. http://dx.doi.org/10.3390/cells8040353.

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The most common cystic fibrosis-causing mutation (F508del, present in ~85% of CF patients) leads to CFTR misfolding, which is recognized by the endoplasmic reticulum (ER) quality control (ERQC), resulting in ER retention and early degradation. It is known that CFTR exit from the ER is mediated by specific retention/sorting signals that include four arginine-framed tripeptide (AFT) retention motifs and a diacidic (DAD) exit code that controls the interaction with the COPII machinery. Here, we aim at obtaining a global view of the protein interactors that regulate CFTR exit from the ER. We used mass spectrometry-based interaction proteomics and bioinformatics analyses to identify and characterize proteins interacting with selected CFTR peptide motifs or full-length CFTR variants retained or bypassing these ERQC checkpoints. We conclude that these ERQC trafficking checkpoints rely on fundamental players in the secretory pathway, detecting key components of the protein folding machinery associated with the AFT recognition and of the trafficking machinery recognizing the diacidic code. Furthermore, a greater similarity in terms of interacting proteins is observed for variants sharing the same folding defect over those reaching the same cellular location, evidencing that folding status is dominant over ER escape in shaping the CFTR interactome.

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Ostapenko, L. "The Biblical Code in the Novel «Windows on the World» by Frédéric Beigbeder." Literature and Culture of Polissya 106, no. 20f (December 12, 2022): 63–75. http://dx.doi.org/10.31654/2520-6966-2022-20f-106-63-75.

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The article represents the interpretation of the novel "Windows on the World" by the modern French writer Frédéric Beigbeder from the point of view of the biblical code. The author of the article distinguishes two levels of the presence of biblical components: explicit and implicit. The author inventories the Old Testament and New Testament images and motifs marked in the work, and she determines their functionality. The author proves that it is the components of the biblical code that perform content-creating and form-creating functions in the novel. The biblical code defines the structure of the novel as parabolic and deepens its dystopian content, giving it an eschatological dominant. The author pays special attention to the transformation of the biblical story about the Tower of Babel in the novel. The author proves that the Old Testament motifs of creation and destruction, which are associated with the image of the Tower of Babel, characterize the consequences of economic and cultural globalization in the novel by Frédéric Beigbeder and acquire an apocalyptic dimension. The writer assigns a special role in the process of globalization to marketing as a means of promoting mass culture, which produces a profaned image of the world and brings humanity closer to its end. The author analyzes the novel’s intertextual connections, which are related to its biblical code. The image of the Catcher from the novel "The Catcher in the Rye" by J. David Salinger deepens the semantics of the biblical code in the novel "Windows on the World." The writer demonstrates that the messianism of the "broken generation" of America, which was represented by JD Salinger, later turned into "superheroism", and the path of spiritual ascent was profaned by the construction of skyscrapers. The author proves that with the help of the biblical code, the writer builds his own eschatological vision of the world, which deviates from the metanarratives of Christianity and globalism and takes away humanity’s last hopes. The apocalypse that Frédéric Beigbeder recreates in the novel "Windows on the World" provides redemption, but it does not guarantee salvation. His "Savior" reminds mankind only of death and it does not promise eternal life to anyone.

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Urbanek-Trzeciak, Martyna, Edyta Jaworska, and Wlodzimierz Krzyzosiak. "miRNAmotif—A Tool for the Prediction of Pre-miRNA–Protein Interactions." International Journal of Molecular Sciences 19, no. 12 (December 17, 2018): 4075. http://dx.doi.org/10.3390/ijms19124075.

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MicroRNAs (miRNAs) are short, non-coding post-transcriptional gene regulators. In mammalian cells, mature miRNAs are produced from primary precursors (pri-miRNAs) using canonical protein machinery, which includes Drosha/DGCR8 and Dicer, or the non-canonical mirtron pathway. In plant cells, mature miRNAs are excised from pri-miRNAs by the DICER-LIKE1 (DCL1) protein complex. The involvement of multiple regulatory proteins that bind directly to distinct miRNA precursors in a sequence- or structure-dependent manner adds to the complexity of the miRNA maturation process. Here, we present a web server that enables searches for miRNA precursors that can be recognized by diverse RNA-binding proteins based on known sequence motifs to facilitate the identification of other proteins involved in miRNA biogenesis. The database used by the web server contains known human, murine, and Arabidopsis thaliana pre-miRNAs. The web server can also be used to predict new RNA-binding protein motifs based on a list of user-provided sequences. We show examples of miRNAmotif applications, presenting precursors that contain motifs recognized by Lin28, MCPIP1, and DGCR8 and predicting motifs within pre-miRNA precursors that are recognized by two DEAD-box helicases—DDX1 and DDX17. miRNAmotif is released as an open-source software under the MIT License. The code is available at GitHub (www.github.com/martynaut/mirnamotif). The webserver is freely available at http://mirnamotif.ibch.poznan.pl.

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El Karkouri, Khalid, Claude Murat, Elisa Zampieri, and Paola Bonfante. "Identification of Internal Transcribed Spacer Sequence Motifs in Truffles: a First Step toward Their DNA Bar Coding." Applied and Environmental Microbiology 73, no. 16 (June 29, 2007): 5320–30. http://dx.doi.org/10.1128/aem.00530-07.

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ABSTRACT This work presents DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat unit which are useful for the identification of five European and Asiatic truffles (Tuber magnatum, T. melanosporum, T. indicum, T. aestivum, and T. mesentericum). Truffles are edible mycorrhizal ascomycetes that show similar morphological characteristics but that have distinct organoleptic and economic values. A total of 36 out of 46 ITS1 or ITS2 sequence motifs have allowed an accurate in silico distinction of the five truffles to be made (i.e., by pattern matching and/or BLAST analysis on downloaded GenBank sequences and directly against GenBank databases). The motifs considered the intraspecific genetic variability of each species, including rare haplotypes, and assigned their respective species from either the ascocarps or ectomycorrhizas. The data indicate that short ITS1 or ITS2 motifs (≤50 bp in size) can be considered promising tools for truffle species identification. A dot blot hybridization analysis of T. magnatum and T. melanosporum compared with other close relatives or distant lineages allowed at least one highly specific motif to be identified for each species. These results were confirmed in a blind test which included new field isolates. The current work has provided a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies.

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Wu, Fang, Dragomir Radev, and Stan Z. Li. "Molformer: Motif-Based Transformer on 3D Heterogeneous Molecular Graphs." Proceedings of the AAAI Conference on Artificial Intelligence 37, no. 4 (June 26, 2023): 5312–20. http://dx.doi.org/10.1609/aaai.v37i4.25662.

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Procuring expressive molecular representations underpins AI-driven molecule design and scientific discovery. The research mainly focuses on atom-level homogeneous molecular graphs, ignoring the rich information in subgraphs or motifs. However, it has been widely accepted that substructures play a dominant role in identifying and determining molecular properties. To address such issues, we formulate heterogeneous molecular graphs (HMGs) and introduce a novel architecture to exploit both molecular motifs and 3D geometry. Precisely, we extract functional groups as motifs for small molecules and employ reinforcement learning to adaptively select quaternary amino acids as motif candidates for proteins. Then HMGs are constructed with both atom-level and motif-level nodes. To better accommodate those HMGs, we introduce a variant of the Transformer named Molformer, which adopts a heterogeneous self-attention layer to distinguish the interactions between multi-level nodes. Besides, it is also coupled with a multi-scale mechanism to capture fine-grained local patterns with increasing contextual scales. An attentive farthest point sampling algorithm is also proposed to obtain the molecular representations. We validate Molformer across a broad range of domains, including quantum chemistry, physiology, and biophysics. Extensive experiments show that Molformer outperforms or achieves the comparable performance of several state-of-the-art baselines. Our work provides a promising way to utilize informative motifs from the perspective of multi-level graph construction. The code is available at https://github.com/smiles724/Molformer.

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Journal articles on the topic 'Motifs du code circulaire'

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