Biology subjects

Bernard, G.

Publications and source records attributed to Bernard, G..

8 recordsLinked to original sources

bioRxiv2025

Bigger is not always better: Optimizing leaf area index with narrow leaf shape in soybean

Modern soybean varieties have higher than optimal leaf area index (LAI), which could divert resources from reproductive growth. Altering leaf shape could be a simple strategy to reduce LAI. To test this, we developed 204 near-isogenic soybean lines differing in leaf morphology by introgressing narrow-leaf alleles from donor parents PI 612713A and PI 547745 into the elite, broad-leaf cultivar LD11-2170. We evaluated the lines across two locations and two row spacings (38-cm and 76-cm) to assess how reduced investment in leaf area influences canopy architecture, crop physiology, and yield. Narrow-leaf lines showed 13% lower peak LAI and 3% lower digital biomass compared to broad-leaf counterparts yet maintained yield parity (5,756 vs. 5.801 kg ha-1, p = 0.43) across environmental conditions. Photosynthetic capacity remained largely unchanged, with narrow-leaf lines showing modest increases in electron transport rate and leaf mass per area. Narrow-leaf lines achieved similar canopy closure timing despite lower LAI, suggesting architectural compensation mechanisms. The most striking difference appeared in seed packaging, with narrow-leaf lines producing 34% four-seeded pods compared to only 1.8% in broad-leaf lines. There was a nonlinear relationship between peak LAI and yield, with optimal LAI values of 9-11 varying by environment. These findings show that the single-gene GmJAG1-controlled narrow-leaf trait offers a tractable strategy for reducing LAI and maintaining high productivity. This could reduce the metabolic costs associated with excessive canopy development and support sustainable agriculture under increasing climate variability.

plant biology↗

bioRxiv2024

Single Cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures

Cellular heterogeneity is a common issue in differentiation protocols of oligodendrocytes (OLs) from human induced pluripotent stem cells. Our previous work described a novel method to generate OLs and highlighted the presence of glial progenitors. Here, we unravel the glial heterogeneity and characterize the response of isolated subpopulations to differentiation. This study provides a novel tool for studying the dynamics of glial development in vitro and on a transcriptomic level.

neuroscience↗

bioRxiv2024

Patterns and drivers of diatom diversity and abundance in the global ocean

Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity was confirmed, and the most prevalent genera were Chaetoceros, Thalassiosira, Actinocyclus and Pseudo-nitzschia. We defined 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection were among the cellular functions in which natural diatom populations invested the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impacts.

ecology↗

bioRxiv2024

Network studies unveil new groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean

BackgroundMetagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known tree of life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters, including at relatively lenient clustering thresholds. ResultsHere, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40 million ORFs predicted in marine environments. We assessed the environmental diversity of 53 gene families as old as cellular life, broadly distributed across the Tree of Life. About half of them harboured clusters of environmental homologues that diverged significantly from the known diversity of published complete genomes, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential genes (SMC), divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases of unknown origin in the ultra-small size fraction. ConclusionsThese results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.

evolutionary biology↗

bioRxiv2023

The Use of a SOX10 Reporter Towards Ameliorating Oligodendrocyte Lineage Differentiation from Human Induced Pluripotent Stem Cells

Oligodendrocytes (OLs) are key players in the central nervous system, critical for the formation and maintenance of the myelin sheaths insulating axons, ensuring efficient neuronal communication. In the last decade, the use of human induced pluripotent stem cells (iPSCs) has become essential for recapitulating and understanding the differentiation and role of OLs in vitro. Current methods include overexpression of transcription factors for rapid OL generation, neglecting the complexity of OL lineage development. Alternatively, growth factor-based protocols offer physiological relevance but struggle with efficiency and cell heterogeneity. To address these issues, we created a novel SOX10-P2A-mOrange iPSC reporter line to track and purify oligodendrocyte precursor cells (OPCs). Using this reporter cell line, we analyzed an existing differentiation protocol and shed light on the origin of glial cell heterogeneity. Additionally, we have modified the differentiation protocol, towards enhancing reproducibility, efficiency, and terminal maturity. Our approach not only advances OL biology but holds promise to accelerate research and translational work with iPSC-derived OLs. Main PointsO_LIThe differentiation of iPSCs in Oligodendrocyte Precursor Cells (OPCs) and Oligodendrocytes (OLs) is a notoriously difficult technique and often displays variable efficiency and cellular heterogeneity. C_LIO_LIWe engineered a novel reporter line carrying the fluorescent protein mOrange under the control of the OL-specific transcription factor SOX10 to track, purify and characterize OLs. C_LIO_LIBy experimenting with diverse differentiation media, we improved the generation of SOX10-positive cells. Consequently, these cells exhibited increased consistency and effectiveness in evolving into myelinating OLs. C_LI

cell biology↗

bioRxiv2023

An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants

The role of non-coding regulatory elements and how they might contribute to tissue type specificity of disease phenotypes is poorly understood. Autosomal Dominant Leukodystrophy (ADLD) is a fatal, adult-onset, neurological disorder that is characterized by extensive CNS demyelination. Most cases of ADLD are caused by tandem genomic duplications involving the lamin B1 gene (LMNB1) while a small subset are caused by genomic deletions upstream of the gene. Utilizing data from recently identified families that carry LMNB1 gene duplications but do not exhibit demyelination, ADLD patient tissues, CRISPR modified cell lines and mouse models, we have identified a novel silencer element that is lost in ADLD patients and that specifically targets overexpression to oligodendrocytes. This element consists of CTCF binding sites that mediate three-dimensional chromatin looping involving the LMNB1 and the recruitment of the PRC2 repressor complex. Loss of the silencer element in ADLD identifies a previously unknown role for silencer elements in tissue specificity and disease causation.

genetics↗

bioRxiv2019

Benchmarking of alignment-free sequence comparison methods

Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events. The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.

bioinformatics↗

bioRxiv2017

K-mer Similarity, Networks Of Microbial Genomes And Taxonomic Rank

Alignment-free (AF) methods have recently been adopted to infer phylogenetic trees. However, the evolutionary relationships among microbes, impacted by common phenomena such as lateral genetic transfer and rearrangement, cannot be adequately captured in a strictly tree-like structure. Bacterial and archaeal genomes consist of highly conserved regions, e.g. ribosomal RNA genes (commonly used as phylogenetic markers), more-variable regions and extrachromosomal elements, i.e. plasmids (that contain genes critical under a selective condition e.g. antibiotic resistance). The impact of these elements on genome-scale inference of microbial phylogeny remains little known. Here, using an AF approach, we inferred phylogenomic networks of microbial life based on 2785 completely sequenced bacterial and archaeal genomes, and systematically assessed the impact of ribosomal RNA genes and plasmid sequences in this network. Our results indicate that k-mer similarity can correlate with taxonomic rank of microbes. Using a relational database approach, we linked the implicated k-mers to annotated genomic regions (thus functions), and defined core functions in specific phyletic groups and genera. We found that, in most phyla, highly conserved functions are often related to Amino acid metabolism and transport, and Energy production and conversion. Our findings indicate that AF phylogenomics can be used to infer reticulate relationships in a scalable manner and provide new perspective into microbial biology and evolution.

evolutionary biology↗