Biology subjects

Leger, T.

Publications and source records attributed to Leger, T..

5 recordsLinked to original sources

bioRxiv2025

High Throughput Information Extraction of Printed Specimen Labels from Large-Scale Digitization of Entomological Collections using a Semi-Automated Pipeline

O_LINatural history museums curate billions of insect specimens, forming a vast but underutilized resource for biodiversity research. While digitization efforts have increased the availability of high-resolution specimen images, extracting metadata from labels remains a major bottleneck, often requiring manual transcription. C_LIO_LIWe developed a semi-automated pipeline, ELIE (Entomological Label Information Extraction), which combines computer vision, convolutional neural networks (CNNs), optical character recognition (OCR), and clustering algorithms to streamline label data extraction. Our pipeline operates in three stages: (1) label detection and classification (printed vs. handwritten), (2) OCR-based text extraction from printed labels using Tesseract or Google Vision, and (3) clustering of extracted text for human validation of outliers. C_LIO_LIBenchmarking on diverse datasets from multiple museum collections showed that our approach successfully extracted and clustered up to 98% of printed labels, significantly reducing manual effort. The pipeline improves efficiency in digitization workflows while maintaining high accuracy in label data capture. C_LIO_LIOur approach demonstrates the potential of integrating AI-driven methods with human validation to accelerate specimen digitization. By reducing manual transcription workload and enabling scalable extraction of insect label metadata, it unlocks biodiversity data for research in ecology, systematics, and conservation globally. C_LI

bioinformatics↗

bioRxiv2022

The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species using morphology and DNA capture in type specimens

Recent developments in museomics enable genetic information to be recovered from previously unusable collection specimens and thus to answer complex taxonomic questions. Here we apply museomics to a taxonomic problem involving several species of Argyria Hubner (Pyraloidea, Crambinae), with previously unrecognized morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, we aimed to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridization capture protocol, we partially recovered the DNA barcode of the lectotype of Argyria lacteella (Fabricius, 1794) for comparison with the 229 DNA barcode sequences of Argyria specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: the Argyria abronalis (Walker, 1859) holotype, thus confirming the synonymy of this name with A. lacteella, the holotype of A. lusella (Zeller, 1863), rev. syn., the holotype of A. multifacta Dyar, 1914, syn. n., newly synonymized with A. lacteella, and a specimen of Argyria diplomochalis Dyar, 1913, collected in 1992. A complementary sampling composed of nine specimens of A. lacteella, A. diplomochalis, A. centrifugens Dyar, 1914 and A. gonogramma Dyar, 1915, from North to South America, were integrated using classical COI amplification and Sanger sequencing. Argyria gonogramma Dyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified as A. lacteella. Following morphological study of its holotype, Argyria vestalis Butler, 1878, syn. n. is also synonymized with A. lacteella. The name A. pusillalis Hubner, 1818, is considered a nomen dubium associated with A. gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted for A. lacteella, A. diplomochalis, A. centrifugens, and A. gonogramma based on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the Antillean A. diplomochalis. Our work highlights the efficiency of the DNA hybrid capture enrichment method to retrieve DNA barcodes from 18th and 19th century type specimens in order to solve taxonomic issues in Lepidoptera.

zoology↗

bioRxiv2021

Insight in the quorum sensing-driven lifestyle of the non-pathogenic Agrobacterium tumefaciens 6N2 and the interactions with the yeast Meyerozyma guilliermondii

Agrobacterium tumefaciens is considered a prominent phytopathogen, though most isolates are nonpathogenic. Agrobacteria can inhabit plant tissues interacting with other microorganisms. Yeasts are likewise part of these communities. We analyzed the quorum sensing (QS) systems of A. tumefaciens strain 6N2, and its relevance for the interaction with the yeast Meyerozyma guilliermondii, both sugarcane endophytes. We show that strain 6N2 is nonpathogenic, produces OHC8-HSL, OHC10-HSL, OC12-HSL and OHC12-HSL as QS signals, and possesses a complex QS architecture, with one truncated, two complete systems, and three additional QS-signal receptors. A proteomic approach showed differences in QS-regulated proteins between pure (64 proteins) and dual (33 proteins) cultures. Seven proteins were consistently regulated by quorum sensing in pure and dual cultures. M. guilliermondii proteins influenced by QS activity were also evaluated. Several up- and down- regulated proteins differed depending on the bacterial QS. These results show the importance of the QS regulation in the bacteria-yeast interactions. HighlightsThe avirulent A. tumefaciens 6N2 has two replicons and a complex QS architecture The profile of QS-regulated proteins is modified in dual cultures with Pa. laurentii The bacterial QS activity alters the proteome of the yeast Pa. laurentii

microbiology↗

bioRxiv2019

Singular manifolds of proteomic drivers to model the evolution of inflammatory bowel disease status

The conditions who denotes the presence of an immune disease are often represented by interaction graphs. These informative, but complex structures are susceptible to being perturbed at different levels. The mode in which that perturbation occurs is still of utmost importance in areas such as reprogramming therapeutics. In this sense, the overall graph architecture is well characterise by module identification. Topological overlap-related measures make possible the localisation of highly specific module regulators that can perturb other nodes, potentially causing the entire system to change behaviour or collapse. We provide a geometric framework explaining such situations in the context of inflammatory bowel diseases (IBD). IBD are important chronic disorders of the gastrointestinal tract which incidence is dramatically increasing worldwide. Our approach models different IBD status as Riemannian manifolds defined by the graph Laplacian of two high throughput proteome screenings. Identifies module regulators as singularities within the manifolds (the so-called singular manifolds). And reinterprets the characteristic IBD nonlinear dynamics as compensatory responses to perturbations on those singularities. Thus, we could control the evolution of the disease status by reconfiguring particular setups of immune system to an innocuous target state.

systems biology↗

bioRxiv2019

Novel Function of Bluetongue Virus NS3 Protein in Regulation of the MAPK/ERK Signaling Pathway

Bluetongue virus (BTV) is an arbovirus transmitted by blood-feeding midges to a wide range of wild and domestic ruminants. In this report, we showed that BTV, through its virulence non-structural protein NS3 (BTV-NS3), is able to activate the MAPK/ERK pathway. In response to growth factors, the MAPK/ERK pathway activates cell survival, differentiation, proliferation and protein translation but can also lead to the production of several inflammatory cytokines. By combining immunoprecipitation of BTV-NS3 and mass spectrometry analysis from both BTV-infected and NS3-transfected cells, we identified the serine/threonine-protein kinase B-Raf (BRAF), a crucial player of the MAPK/ERK pathway, as a new cellular interactor of BTV-NS3. BRAF silencing led to a significant decrease of the MAPK/ERK activation by BTV supporting a model where BTV-NS3 interacts with BRAF to activate this signaling cascade. Furthermore, the intrinsic ability of BTV-NS3 to bind BRAF and activate the MAPK/ERK pathway is conserved throughout multiple serotypes/strains but appears to be specific to BTV compared to other members of Orbivirus genus. Inhibition of MAPK/ERK pathway with U0126 reduced viral titers, suggesting that BTV manipulates this pathway for its own replication. Therefore, the activation of the MAPK/ERK pathway by BTV-NS3 could benefit to BTV replication by promoting its own viral protein synthesis but could also explain the deleterious inflammation associated with tissue damages as already observed in severe cases of BT disease. Altogether, our data provide molecular mechanisms to explain the role of BTV-NS3 as a virulence factor and determinant of pathogenesis. ImportanceBluetongue Virus (BTV) is responsible of the non-contagious arthropod-borne disease Bluetongue (BT) transmitted to ruminants by blood-feeding midges. Despite the fact that BTV has been extensively studied, we still have little understanding of the molecular determinants of BTV virulence. In this report, we found that the virulence protein NS3 interacts with BRAF, a key component of the MAPK/ERK pathway. In response to growth factors, this pathway promotes cell survival, increases protein translation but also contributes to the production of inflammatory cytokines. We showed that BTV-NS3 enhances the MAPK/ERK pathway and this activation is BRAF-dependent. Our results demonstrate, at the molecular level, how a single virulence factor has evolved to target a cellular function to ensure its viral replication. On the other hand, our findings could also explain the deleterious inflammation associated with tissue damages as already observed in severe cases of BT disease.

microbiology↗