IMGT/mAb-KG: the knowledge graph for therapeutic monoclonal antibodies

IntroductionTherapeutic monoclonal antibodies (mAbs) have demonstrated promising outcomes in diverse clinical indications, including but not limited to graft rejection, cancer, and autoimmune diseases lately.Recognizing the crucial need for the scientific community to quickly and easily access dependable information on monoclonal antibodies (mAbs), IMGT®, the international ImMunoGeneTics information system®, provides a unique and invaluable resource: IMGT/mAb-DB, a comprehensive database of therapeutic mAbs, accessible via a user-friendly web interface. However, this approach restricts more sophisticated queries and segregates information from other databases.MethodsTo connect IMGT/mAb-DB with the rest of the IMGT databases, we created IMGT/mAb-KG, a knowledge graph for therapeutic monoclonal antibodies connected to IMGT structures and genomics databases. IMGT/mAb-KG is developed using the most effective methodologies and standards of semantic web and acquires data from IMGT/mAb-DB. Concerning interoperability, IMGT/mAb-KG reuses terms from biomedical resources and is connected to related resources.Results and discussionIn February 2024, IMGT/mAb-KG, encompassing a total of 139,629 triplets, provides access to 1,489 mAbs, approximately 500 targets, and over 500 clinical indications. It offers detailed insights into the mechanisms of action of mAbs, their construction, and their various products and associated studies. Linked to other resources such as Thera-SAbDab (Therapeutic Structural Antibody Database), PharmGKB (a comprehensive resource curating knowledge on the impact of genetic variation on drug response), PubMed, and HGNC (HUGO Gene Nomenclature Committee), IMGT/mAb-KG is an essential resource for mAb development. A user-friendly web interface facilitates the exploration and analyse of the content of IMGT/mAb-KG

The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae

<p>Abstract</p> <p>Background</p> <p>The <it>Xanthomonadaceae </it>family contains two xylem-limited plant pathogenic bacterial species, <it>Xanthomonas albilineans </it>and <it>Xylella fastidiosa</it>. <it>X. fastidiosa </it>was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess <it>hrp </it>genes which encode a Type III secretion system found in most plant pathogenic bacteria. <it>X. fastidiosa </it>was excluded from the <it>Xanthomonas </it>group based on phylogenetic analyses with rRNA sequences.</p> <p>Results</p> <p>The complete genome of <it>X. albilineans </it>was sequenced and annotated. <it>X. albilineans</it>, which is not known to be insect-vectored, also has a reduced genome and does not possess <it>hrp </it>genes. Phylogenetic analysis using <it>X. albilineans </it>genomic sequences showed that <it>X. fastidiosa </it>belongs to the <it>Xanthomonas </it>group. Order of divergence of the <it>Xanthomonadaceae </it>revealed that <it>X. albilineans </it>and <it>X. fastidiosa </it>experienced a convergent reductive genome evolution during their descent from the progenitor of the <it>Xanthomonas </it>genus. Reductive genome evolutions of the two xylem-limited <it>Xanthomonadaceae </it>were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens.</p> <p>Conclusion</p> <p>The two xylem-limited <it>Xanthomonadaceae</it>, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of <it>X. albilineans </it>differ from those of <it>X. fastidiosa </it>and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by <it>X. albilineans</it>, is discussed.</p

Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)

Background \ud Land plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown to participate in post-transcriptional events involved in organellar gene expression, and this type of function is now thought to be their main biological role. Among PPR genes, restorers of fertility (Rf) of cytoplasmic male sterility systems constitute a peculiar subgroup that is thought to evolve in response to the presence of mitochondrial sterility-inducing genes. Rf genes encoding PPR proteins are associated with very close relatives on complex loci. \ud Results \ud We sequenced a non-restoring allele (L7rfo) of the Rfo radish locus whose restoring allele (D81Rfo) was previously described, and compared the two alleles and their PPR genes. We identified a ca 13 kb long fragment, likely originating from another part of the radish genome, inserted into the L7rfo sequence. The L7rfo allele carries two genes (PPR-1 and PPR-2) closely related to the three previously described PPR genes of the restorer D81Rfo allele (PPR-A, PPR-B, and PPR-C). Our results indicate that alleles of the Rfo locus have experienced complex evolutionary events, including recombination and insertion of extra-locus sequences, since they diverged. Our \ud analyses strongly suggest that present coding sequences of Rfo PPR genes result from intragenic recombination. We found that the 10 C-terminal PPR repeats in Rfo PPR gene encoded proteins result from the tandem duplication of a 5 PPR repeat block. \ud Conclusions \ud The Rfo locus appears to experience more complex evolution than its flanking \ud sequences. The Rfo locus and PPR genes therein are likely to evolve as a result of \ud intergenic and intragenic recombination. It is therefore not possible to determine which genes on the two alleles are direct orthologs. Our observations recall some \ud previously reported data on pathogen resistance complex loci. \u

História e historiadores na vulgarização científica do Brasil oitocentista: as “Conferências Populares da Glória”

This paper aims to understand the place of History and historians in the Gloria Popular Conferences – considered by the historiography as one of the most important and ambitious Science Communication projects in Brazil during the 19th century. For that, the profiles, themes, and approaches of History lecturers held between 1873-1880 were analyzed, indicating that historical themes played an expressive role on the Gloria Popular Conferences. Moreover, the results show that historians and the represented History were aligned with the historiographic purposes of Instituto Histórico e Geográfico Brasileiro (IHGB), whereby History, as well as other humanities and natural sciences, met the public education criteria that guided the project from its beginning.O objetivo deste trabalho é compreender que lugar a história e os “historiadores” ocuparam nas Conferências Populares da Glória, considerada pela literatura especializada como um marco da “vulgarização científica” do Brasil oitocentista. Para esse fim, serão examinados os perfis dos principais “conferencistas de história”, as temáticas dessas conferências e o teor de algumas dessas falas. Considera-se neste estudo o período 1873-1880, e o corpus documental é formado por resumos e transcrições das conferências publicadas em jornais e revistas do Rio de Janeiro. A análise evidenciou que um dos mais importantes eventos de vulgarização científica do Brasil no século XIX reservou um lugar expressivo para temas históricos e que os “historiadores” e a “história” aí representados estavam alinhados com as perspectivas históricas predominantes no Instituto Histórico e Geográfico Brasileiro (IHGB), estando a história, a exemplo de outras humanidades e ciências da natureza, a serviço do projeto de instrução pública que orientou, desde o início, as Conferências Populares da Glória

A Figura do Intelectual e a Razão Universal na Fundação do Instituto Histórico e Geográfico Brasileiro

Este ensaio apresenta um estudo sobre a articulação da biografia coletiva dos fundadores do Instituto Histórico e Geográfico Brasileiro e de sua Revista com a política cultural do Estado imperial brasileiro, em que se observa, sobretudo, como o perfil dos membros do Instituto conformava determinada figura de intelectual através de sua rede de sociabilidades, sua mentalidade civilizatória e a cultura política de sua geração. O objetivo é evidenciar que o significado do intelectual no contexto da fundação do IHGB se define através de um discurso que une a fala em nome da razão, da humanidade e da civilização, à fala em nome do Estado e da nação.This essay presents a study on the articulation of the collective biography of the Brazilian Historical and Geographical Institute’s founders and of its journal with the cultural politic of the Brazilian emperor state, in which is observed, above all, how the Institute members’ profile fitted certain image of intellectual through its sociability network, its civilizing mentality and the political culture of its generation. The objective is to outline that the meaning of the intellectual in the context of the foundation of the Brazilian Historical and Geographical Institute is defined through a discourse that unify the speech on the behalf of reason, of humanity  and of civilization, with the speech on the behalf of the state and of the nation

First Elements on Knowledge Discovery guided by Domain Knowledge (KDDK)

International audienceIn this paper, we present research trends carried out in the Orpailleur team at Loria, showing how knowledge discovery and knowledge processing may be combined. The knowledge discovery in databases process (KDD) consists in processing a huge volume of data for extracting significant and reusable knowledge units. From a knowledge representation perspective, the KDD process may take advantage of domain knowledge embedded in ontologies relative to the domain of data, leading to the notion of ''knowledge discovery guided by domain knowledge'' or KDDK. The KDDK process is based on the classification process (and its multiple forms), e.g. for modeling, representing, reasoning, and discovering. Some applications are detailed, showing how KDDK can be instantiated in an application domain. Finally, an architecture of an integrated KDDK system is proposed and discussed

Possibilidades do uso de canções no ensino-aprendizagem de francês língua estrangeira

Este trabalho tem como tema a canção no ensino de Francês Língua Estrangeira. Seu objetivo é pesquisar possibilidades de trabalhar a canção em sala de aula de FLE, abordando aspectos linguísticos, musicais e histórico-sociais da canção. O referencial teórico inclui autores da área da canção, como Beaumont James (1999), Calvet (1974, 1980, 2006, 2013) e Tatit (2002), e da pedagogia, como Boiron (2001, 2003, 2012), Tagliante (2006), Lemeunier (2006) e Gourvennec (2017). A conclusão reforça a ideia de que a canção é um documento autêntico com múltiplas possibilidades de utilização em sala de aula de línguas. No último capítulo, há uma ficha passe-partout com ideias de atividades para a utilização de canções em sala de aula de línguas. Esta ficha foi elaborada com o objetivo de contribuir para a reflexão sobre o uso de canções na didática de Francês Língua Estrangeira. Finaliza este trabalho um exemplo de ficha pedagógica utilizando canções.Ce travail a pour thème la chanson dans l'enseignement du français langue étrangère ; son objectif est de rechercher les possibilités de travailler la chanson en classe de FLE, en abordant les aspects linguistiques, musicaux et historico-sociaux de la chanson. Le cadre théorique inclut des auteurs issus du domaine de la chanson, tel quel Beaumont-James (1999), Calvet (1974, 1980, 2006, 2013) et Tatit(2002) et de la pédagogie, comme Boiron (2001, 2003, 2012), Tagliante (2006), Lemeunier (2006) et Gourvennec (2017). La conclusion renforce l'idée que la chanson est un document authentique aux multiples possibilités d'utilisation en salle de classe de langues. Dans le dernier chapitre, il y a une fiche passe-partout avec des idées d'activités pour utiliser des chansons en classe de langue. Cette fiche a été créée dans le but de contribuer à la réflexion sur l’utilisation des chansons en didactique de FLE. Ce travail se termine par un exemple de fiche pédagogique utilisant des chansons

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Abstract\ud \ud \ud \ud Background\ud Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences.\ud \ud \ud \ud Results\ud Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations.\ud \ud \ud \ud Conclusions\ud This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.AI is funded by a PhD grant from INRA-SPE and region Pays de la Loire, France. EG was funded by a PhD grant from the French Ministry of National Education and Research and French Guyana. SC, EG, MA, EL and LDN are funded by the LABEX TULIP (ANR-10-LABX-41), LSG is funded by ANR-2010-GENM-013 Xanthomix