Biology subjects

Bray, F.

Publications and source records attributed to Bray, F..

8 recordsLinked to original sources

bioRxiv2026

Detection of bifidobacterial lipoproteins with anti-viral potential in donor human milk

Background: Group B coxsackieviruses (CVBs) are involved in triggering type 1 diabetes. Free bifidobacterial lipoproteins (BLps) prevent CVBs cell infection. Our objective is to isolate free BLps potentially released by bifidobacteria in breastmilk and document their bioavailability. Methods: Bifidobacterium breve and B. longum were quantified by qPCR in samples donated to the hospitals biobank (DHM) within two weeks following delivery. BLps were captured onto CV B4, analyzed by SDS-PAGE and competitive ELISA. BLps transport through Caco-2 monolayers was monitored after DHM contact. Titration of anti-CV B IgA was carried out by ELISA. Results: Among the 90 enrolled donors, seven were excluded, 68 donated a unique sample and 15 donated multiple specimens (2 to 12). B. breve and B.longum were detected in 93.0 % and 32.8% unique DHM samples, respectively. The two species showed unstable counts in the multiple donation group. Although at highly variable amounts, BLps were readily detected. Free B.longum Lps were found in absence of B.longum itself. The BLps crossed the cell layer within 4h still binding CV B4. Conclusion: DHM contained BLps able to cross a cell layer mimicking the intestine still retaining their capacity to bind CV B. It suggested a possible newborns systemic protection against CV B4 infection that needs further investigation.

microbiology↗

bioRxiv2026

High-throughput targeted paleoproteomics sex estimation on medieval Great Moravia individuals using MALDI-CASI-FTICR mass spectrometry

The estimation of the biological sex of archeological remains is crucial information in bioarchaeology and forensic anthropology. In recent years, proteomics based on molecular sexual dimorphism have emerged as a preferred method, particularly because of its minimally-invasive approach to extracting amelogenin X and Y proteins from tooth enamel. However, there is an increasing demand to accelerate this process while facilitating the analysis of large archaeological assemblages. This study presents a novel high-throughput targeted paleoproteomics method for biological sex estimation using MALDI-CASI-FTICR mass spectrometry. This approach combines the strengths of existing methods, including ultra-high resolution, significantly reduced processing times, targeted analysis, and scalability to large archaeological sample sets. The method was initially validated on modern individuals with known sex and subsequently applied to 130 adult and juvenile individuals from medieval Great Moravia (present-day Czech Republic). Biological sex was successfully estimated for all but one of the individuals. The results not only provide a more efficient biological sex estimation but also help to resolve a few errors in sex assessment previously encountered with osteomorphological and tooth morphometric techniques. The implementation of this method significantly improves the accuracy and efficiency of biological sex estimation, offering a powerful tool for anthropological research. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/706309v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1ede7e6org.highwire.dtl.DTLVardef@13d2f5org.highwire.dtl.DTLVardef@17ee44dorg.highwire.dtl.DTLVardef@1be9dd9_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2026

Time-Resolved Analysis of the Cell Wall Proteome in Saccharomyces cerevisiae S288c During Batch Fermentation

The yeast cell wall is a highly dynamic and multifunctional structure that is essential for maintaining cellular integrity, protecting against environmental stresses, and enabling adhesion, signaling, and interactions with the surrounding environment. Its chemical composition and organization are strongly influenced by external factors such as temperature, pH, nutrient availability and their delivery mode. In batch culture systems, yeast cells grow in a closed environment with limited nutrients, leading to well-defined growth phases that reflect major metabolic transitions. While global proteomic changes during these phases have been described, the temporal regulation of cell wall protein (CWP) expression remains insufficiently characterized. In this study, the temporal remodeling of the cell wall proteome of Saccharomyces cerevisiae S288c was examined during batch cultivation in rich medium over 24 hours. A classical proteomics workflow was applied to analyze CWPs from samples collected at multiple time points over the cultivation period. The analysis revealed substantial qualitative and quantitative changes in CWPs expression linked to metabolic shifts between growth phases. Proteins involved in cell wall remodeling and glycoprotein biosynthesis were particularly enriched at the initial sampling point (b-T0h), corresponding to the transition from flask cultivation to bioreactor conditions, and overall CWP abundance was highest during this early growth stage. Time-resolved quantitative, transcription factor, and functional enrichment analyses revealed coordinated regulation of cell wall adaptation. Stationary-phase specific protein markers linked to glucose depletion were identified, offering insight into nutrient-limited remodeling. Comparisons with previous studies showed variability driven by strain differences, culture conditions, and methodological approaches.

cell biology↗

bioRxiv2025

LIKE EARLY STARVATION is involved in the regulation of starch initiation in potato (Solanum tuberosum cv. Desiree) tubers

Starch initiation has been intensively investigated. In tubers of Solanum tuberosum, it is controlled by a heteromultimeric isoamylase complex composed of ISA1 and ISA2. Moreover, two non-catalytic starch binding proteins (i.e., ESV1 and LESV) regulate leaf starch metabolism in Arabidopsis. Both proteins interact with starch glucans through a C-terminal antiparallel {beta}-sheet domain and differ by the presence of a 115 amino acid N-terminal overhang in LESV. Here we report the CRIPSR/Cas9 inactivation of LESV or ESV1 in potato and the characterization of the respective tuber starches. Starch from esv1 mutants was unaffected whereas granule diameter was severely reduced in tubers of lesv plants. This was negatively correlated to the number of granules, coherent with an altered starch initiation phenotype. Strikingly, scanning electron microscopy of purified starches revealed that lesv plants phenocopy isa1 and isa2 antisense lines described 20 years ago. A physical interaction between LESV and ISA1 was previously demonstrated in rice. Here, we confirmed this interaction in potato using yeast two-hybrid assays, providing molecular evidence for their functional association in potato. This interaction supports the hypothesis that LESV acts in concert with the ISA1/ISA2 complex, likely regulating the early steps of glucan organization required for proper starch granule formation.

plant biology↗

bioRxiv2024

ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation

LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse datasets containing only a few collagen proteins, rendering target-decoy strategies unusable and increasing uncertainty in peptide annotation. ClassiCOL embraces and even extends this ambiguity using a novel isoBLAST approach. The exhaustive set of potential peptide candidates created in this way is then used to retain or reject different potential paths at each taxonomic branching point down to the taxonomic level attainable with the sample information, always allowing for potential mixtures in the process. As an end point, all considered ambiguity is graphically represented with a clear prioritization of the species in the sample. Using public as well as in-house data, we demonstrate the performance of this universal postprocessing approach on different instruments and explore the possibility of identifying genetic as well as sample mixtures. Diet reconstruction from 40,000 year old cave hyena coprolites illustrates the exciting potential of this approach. TeaserClassiCOL is a postprocessing tool that allows for more accurate species classification from LC-MS/MS measurements of collagen.

bioinformatics↗

bioRxiv2023

Low-invasive sampling method for taxonomic for the identification of archaeological and paleontological bones by proteomics of their collagens

Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon and paleoproteomic analyzes, to provide information on diet, dating and taxonomy. Current paleoproteomics methods are destructive and require from a few milligrams to several tenths of milligrams of bone for analysis. In many cultures, bones are raw materials for artefact which are conserved in museum which hampers to damage these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape-discs for sampling. The sampled bone micro-powders were digested following our highly optimized eFASP protocol, then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be performed at archaeological sites or in museums.

paleontology↗

bioRxiv2021

How much does it take to be old? Modelling the time since the last harvesting to infer the distribution of mature forests in France

AimThe distribution of overmature forests in metropolitan France is poorly known, with only a few well-studied prominent sites, and has never been evaluated countrywide. Here, we modelled French forest reserves time since the last harvesting operation - a proxy for forest maturity - then inferred the current statistical distribution of overmature forests (i.e. forests over 50 years without harvesting) in France. LocationMetropolitan France MethodsWe used inventories from forest reserves and managed forests to calibrate a generalised linear mixed model explaining the time since the last harvesting with selected structural attributes and environmental variables. We then projected this model on the independent National Forest Inventory dataset. We thus obtained an updated estimation of the proportion and a rough distribution of overmature forest stands in metropolitan France. ResultsWe found that high basal area of very large trees, high volumes of standing and downed deadwood, high diversity of tree-related microhabitats and more marginally diversity of decay stages best characterized the time since the last harvesting. Volumes of stumps and high density of coppices translating legacy of past forest management also distinguished more overmature plots. Our projection yielded an estimated 3% of French forests over 50 years without harvesting mostly located in more inaccessible areas (i.e. mountainous areas) and a promising proportion of future overmature forests if left unharvested. Main conclusionsOur study showed that the time since the last harvesting is a good proxy for a combination of stand structure attributes key in characterising overmature temperate forests. It gives the first robust statistical estimate of the proportion of overmature forests and may serve to report on their status in metropolitan France. Our method could be implemented at a larger spatial scale, notably in countries with accessible National Forest Inventory and calibration data, to produce indicators at international level.

ecology↗

bioRxiv2020

Substitution of nucleotide-sugar by trehalose-dependent glycogen synthesis pathways in Chlamydiales underlines an unusual requirement for storage polysaccharides within obligate intracellular bacteria

All obligate intracellular pathogens or symbionts of eukaryotes lack glycogen metabolism. Most members of the Chlamydiales order are exceptions to this rule as they contain the classical GlgA-GlgC-dependent pathway of glycogen metabolism that relies on the ADP-Glucose substrate. We surveyed the diversity of Chlamydiales and found glycogen metabolism to be universally present with the important exception of Criblamydiaceae and Waddliaceae families that had been previously reported to lack an active pathway. However, we now find elements of the more recently described GlgE maltose-1-P-dependent pathway in several protist-infecting Chlamydiales. In the case of Waddliaceae and Criblamydiaceae, the substitution of the classical pathway by this recently proposed GlgE pathway was essentially complete as evidenced by the loss of both GlgA and GlgC. Biochemical analysis of recombinant proteins expressed from Waddlia chondrophila and Estrella lausannensis established that both enzymes do polymerize glycogen from trehalose through the production of maltose-1-P by TreS-Mak and its incorporation into glycogens outer chains by GlgE. Unlike Mycobacteriaceae where GlgE-dependent polymerization is produced from both bacterial ADP-Glc and trehalose, glycogen synthesis seems to be entirely dependent on host supplied UDP-Glc and Glucose-6-P or on host supplied trehalose and maltooligosaccharides. These results are discussed in the light of a possible effector nature of these enzymes, of the chlamydial host specificity and of a possible function of glycogen in extracellular survival and infectivity of the chlamydial elementary bodies. They underline that contrarily to all other obligate intracellular bacteria, glycogen metabolism is indeed central to chlamydial replication and maintenance.

microbiology↗