Late Triassic traversodontids (Synapsida: Cynodontia) in southern Africa

Scalenodontoides macrodontes was described in 1957 by Crompton & Ellenberger as a new genus and species of the family Traversodontidae. For many years it was known only by its type specimen, a lower jaw from the Upper Triassic of Lesotho. The specimen was redescribed in more detail by Hopson in 1984, who established the close affinities of Scalenodontoides with Exaeretodon. In 1993, Gow & Hancox described the first skull of Scalenodontoides, discovered, together with fragmentary remains, in South Africa. The skull from South Africa looked very much like a skull from Lesotho, housed in the Muséum National d’Histoire Naturelle, Paris, and initially attributed, in an unpublished work, to the chiniquodontid Belesodon (Costedoat, 1962). Further preparation of the skull from Lesotho was carried out; the specimen proved not to belong to a chiniquodontid, but to a large traversodontid, described in this paper. A revision of the traversodont remains known from the Late Triassic lower Elliot Formation of Lesotho and South Africa leads to the conclusion that they can all be attributed to the species Scalenodontoides macrodontes. Detailed comparisons between Scalenodontoides and Exaeretodon confirm Scalenodontoides as a valid genus, with only one species, Scalenodontoides macrodontes. A new diagnosis of Scalenodontoides macrodontes, based on an analysis of all available material, is given

The Innate Immune Database (IIDB)

<p>Abstract</p> <p>Background</p> <p>As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site <url>http://www.innateImmunity-systemsbiology.org</url>. Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens.</p> <p>Description</p> <p>We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser.</p> <p>Conclusion</p> <p>We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at <url>http://db.systemsbiology.net/IIDB</url>.</p

Shannon Information Theory and Molecular Biology

The role and the contribution of Shannon Information Theory to the development of Molecular Biology has been the object of stimulating debates during the last thirty years. This seems to be connected with some semantic charms associated with the use of the word \u201cinformation\u201d in the biological context. Furthermore information itself, if viewed in a broader perspective, is far from being completely defined in a fashion that overcomes the technical level at which the classical Information Theory has been conceived. This review aims at building on the acknowledged contribution of Shannon Information Theory to Molecular Biology, so as to discover if it is only a technical tool to analyze DNA and proteinic sequences, or if it can rise, at least in perspective, to a higher role that exerts an influence on the construction of a suitable model for handling the genetic information in Molecular Biology

The immunopeptidome from a genomic perspective:Establishing the noncanonical landscape of MHC class I–associated peptides

G.B., D.B., K.W., A.P., R.F., T.R.H., S.K., and J.A.A. received support from Fundacja na rzecz Nauki Polskiej (FNP) (grant ID: MAB/3/2017). D.R.G. received support from Genome Canada & Genome BC (grant ID: 264PRO). D.J.H. received support from NuCana plc (grant ID: SMD0-ZIUN05). H.A. received support from Swedish Cancer Foundation (grant ID: 211709). H.G. received support from United Kingdom Research and Innovation (UKRI) (grant ID: EP/S02431X/1). C.P. received support from Fundação para a Ciência e a Tecnologia (FCT) through LASIGE Research Unit (grant ID: UIDB/00408/2020 and UIDP/00408/2020). A.L. F.M.Z., C.P., A.R., A.P., and J.A.A. received support from European Union’s Horizon 2020 research and innovation programme (grant ID: 101017453). C.B. received support from Agence Nationale de la Recherche (ANR) through GRAL LabEX (grant ID: ANR-10-LABX-49-01) and CBH-EUR-GS 32 (grant ID: ANR-17-EURE0003). S.N.S. received support from Cancer Research UK (CRUK) and the Chief Scientist's Office of Scotland (CSO): Experimental Cancer Medicine Centre (ECMC) (grant ID: ECMCQQR-2022/100017). A.L. received support from Chief Scientist's Office of Scotland (CSO) NRS Career Researcher Fellowship. R.O.N. received support from CRUK Cambridge Centre Thoracic Cancer Programme (grant ID: CTRQQR-2021\100012).Tumor antigens can emerge through multiple mechanisms, including translation of non-coding genomic regions. This non-canonical category of antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry to enable the discovery of non-canonical MHC-associated peptides (ncMAPs) from non-coding regions. Considering that the emergence of tumor antigens can also involve post-translational modifications, we included an open search component in our pipeline. Leveraging the wealth of mass spectrometry-based immunopeptidomics, we analyzed 26 MHC class I immunopeptidomic studies of 9 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant post-translational modifications, using spectral matching and controlled their false discovery rate (FDR) to 1%. Interestingly, the non-canonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 54.85%. Here, we reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targeting agents for T-cell therapies or vaccine development.Publisher PDFPeer reviewe

Independent Origins of Cultivated Coconut (Cocos nucifera L.) in the Old World Tropics

As a portable source of food, water, fuel, and construction materials, the coconut (Cocos nucifera L.) played a fundamental role in human migrations and the development of civilization across the humid tropics. Here we investigated the coconut's domestication history and its population genetic structure as it relates to human dispersal patterns. A sample of 1,322 coconut accessions, representing the geographical and phenotypic diversity of the species, was examined using ten microsatellite loci. Bayesian analyses reveal two highly genetically differentiated subpopulations that correspond to the Pacific and Indo-Atlantic oceanic basins. This pattern suggests independent origins of coconut cultivation in these two world regions, with persistent population structure on a global scale despite long-term human cultivation and dispersal. Pacific coconuts show additional genetic substructure corresponding to phenotypic and geographical subgroups; moreover, the traits that are most clearly associated with selection under human cultivation (dwarf habit, self-pollination, and “niu vai” fruit morphology) arose only in the Pacific. Coconuts that show evidence of genetic admixture between the Pacific and Indo-Atlantic groups occur primarily in the southwestern Indian Ocean. This pattern is consistent with human introductions of Pacific coconuts along the ancient Austronesian trade route connecting Madagascar to Southeast Asia. Admixture in coastal east Africa may also reflect later historic Arab trading along the Indian Ocean coastline. We propose two geographical origins of coconut cultivation: island Southeast Asia and southern margins of the Indian subcontinent

Global Taxonomic Diversity of Anomodonts (Tetrapoda, Therapsida) and the Terrestrial Rock Record Across the Permian-Triassic Boundary

The end-Permian biotic crisis (∼252.5 Ma) represents the most severe extinction event in Earth's history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids (‘mammal-like reptiles’), through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction) indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates

Late Triassic cynodonts from Saint-Nicolas-de-Port (north-eastern France)

De nombreuses dents isolées de cynodontes ont été découvertes dans le Trias supérieur de Saint-Nicolas-de-Port (nord-est de la France). Le matériel étudié est très diversifié et les taxa suivants sont représentés : Pseudotriconodon wildi Hahn, Lepage et Wouters, 1984, Tricuspes tuebingensis E. v. Huene, 1933 ; Tricuspes sigogneauae Hahn, Hahn et Godefroit, 1994 ; Tricuspes tapeinodon n.sp. ; Meurthodon gallicus Sigogneau-Russell et Hahn, 1994 ; Hahnia obliqua n.g., n.sp. ; Gaumia longiradicata Hahn, Wild et Wouters, 1987 ; Lepagia gaumensis, Hahn, Wild et Wouters, 1987 ; Maubeugia lotharingica n.g., n.sp. ; Rosieria delsatei n.g., n.sp. et aff. Microscalenodon. La faune de cynodontes est surtout composée de petits insectivores, représentés notamment par les Dromatheriidae ; de minuscules herbivores, formes naines de la famille des Traversodontidae, sont également présents. L\u27étude de la répartition paléogéographique et stratigraphique des cynodontes du Trias supérieur et du Jurassique inférieur montre que la faune de Saint-Nicolas-de-Port est caractéristique de la période Norien supérieur-Rhétien ; c\u27est incontestablement la faune la plus représentative de cette période pour l\u27Europe de L\u27Ouest. L\u27analyse granulométrique du sédiment du bone-bed a révélé qu\u27il s\u27était accumulé dans un environnement marin proche du rivage.Numerous isolated cynodont teeth have been collected from the Late Triassic of Saint-Nicolas-de-Port (north-eastern France). The material is very diversified and the following taxa are recognized: Pseudotriconodon wildi Hahn, Lepage et Wouters, 1984, Tricuspes tuebingensis E. v. Huene, 1933; Tricuspes sigogneauae Hahn, Hahn et Godefroit, 1994; Tricuspes tapeinodon n.sp.; Meurthodon gallicus Sigogneau-Russell et Hahn, 1994; Hahnia obliqua n.g., n.sp.; Gaumia longiradicata Hahn, Wild et Wouters, 1987; Lepagia gaumensis, Hahn, Wild et Wouters, 1987; Maubeugia lotharingica n.g., n.sp.; Rosieria delsatei n.g., n.sp. and aff. Microscalenodon. This cynodont fauna mainly includes small insectivorous forms, more particularly represented by Dromatheriidae; tiny herbivorous are represented by rare dwarf Traversodontidae. The study of the palaeogeographical and stratigraphic distribution of the Late Triassic to Early Jurassic cynodonts indicates that the fauna discovered in Saint-Nicolas-de-Port is characteristic of the Late Norian-Rhaetian period and is actually the most representative of this period for Western Europe. Granulomatric analysis of the bone-bed reveals that they accumulated in a nearshore shallow marine environment.</p