Diagnosing plague in 17th century camelids from Romania along historical Silk Routes.

Six camels exhumed from a 17th-century Silk Route site in Romania, along with negative controls, were blindly investigated via dental pulp paleometagenomics and paleoproteomics for traces of Yersinia pseudotuberculosis complex including the plague agent Yersinia pestis. Specific reads were detected in sample R04 (one read) and R05 (two reads) which also yielded a 16S rRNA guanine transferase specific for Y. pestis and one other Y.

Phosphate availability modulates the weathering effectiveness and molecular response of Caballeronia mineralivorans PML1(12).

Backgrounds: Minerals and rocks are important reservoirs of nutrients for the soil biota because of their nutritive contents of P, K or Mg. In nutrient-poor environments such as forest soils, microorganisms capable of mobilizing these nutrients gain an ecological advantage. Acidification-based mineral weathering is one of the mechanisms used by these bacteria, but the molecular players involved and their regulation remain poorly characterized.

Wood decay under anoxia by the brown-rot fungus Fomitopsis pinicola.

Basidiomycete fungi are the main decomposers of dead wood with an impact on the global carbon cycle. Their degradative mechanisms have been well-studied under aerobic conditions. Here, we study their activity in oxygen-depleted environments.

Stress resilience in and under harsh drought and/or heat conditions: selected genes, proteins, and lipid integrated responses.

Climate change has intensified the frequency, severity, and simultaneous incidence of drought and heat events, threatening the sustainability of agricultural systems worldwide. This implies the use of resilient plant genotypes able to activate defense mechanisms and overcome stress damage. We examined the leaf transcriptomic, proteomic, and membrane lipid responses in two cultivars of the main coffee-producing species- L.

Molecular and genotoxic effects of carbamazepine and methylmercury on the gonads of Dreissena polymorpha.

Carbamazepine (CBZ) and methylmercury (MeHg) are pervasive contaminants that share molecular toxicity pathways (e.g., neurotoxicity, oxidative stress, energy metabolism) and, in addition to their main toxicity target, are both suspected of reprotoxicity.

Achromobacter xylosoxidans modulates Pseudomonas aeruginosa virulence through a complex multi-target competition.

The colonization and persistence of Pseudomonas aeruginosa in chronically diseased lungs are driven by various virulence factors. However, pulmonary infections in cystic fibrosis (CF) patients are predominantly polymicrobial. While Achromobacter xylosoxidans is an opportunistic pathogen in these patients, its impact on P.

Novel purine derivatives mitigate hypoxia ischemia related brain injury through agrin, zyxin and synaptotagmin proteins.

Hypoxic-ischemic encephalopathy (HIE) is a major cause of morbidity and mortality in newborns resulting in motor and cognitive impairment. Therapeutic hypothermia is the only treatment approved for HIE. Consequently, there is a critical requirement for additional treatments for hypoxic-ischemic (HI) brain injury because hypothermia is only partially protective.

Comprehensive multi-omics integration to unravel poplar molecular responses to a phenanthrene contamination gradient.

Phytoremediation using trees has become popular due to its effectiveness and affordability, including for brownfield soils contaminated with polycyclic aromatic hydrocarbons (PAH). However, our understanding of how trees cope with exposure to PAHs is limited. In this study, we employed an innovative experimental design combining a contamination gradient of eight phenanthrene concentrations (0-2000 mg·kg⁻¹), a model PAH, with a comprehensive integrative multi-omics approach (transcriptomics, proteomics, and metabolomics) to study the physiological responses of poplar (Populus x canadensis).

The microbiologist's guide to metaproteomics.

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics.

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes.

One Health seeks to integrate and balance the health of humans, animals, and environmental systems, which are intricately linked through microbiomes. These microbial communities exchange microbes and genes, influencing not only human and animal health but also key environmental, agricultural, and biotechnological processes. Preventing the emergence of pathogens as well as monitoring and controlling the composition of microbiomes through microbial effectors including virulence factors, toxins, antibiotics, non-ribosomal peptides, and viruses holds transformative potential.

Transcriptomic and proteomic insights into feather keratin degradation by .

Keratin, one of the most recalcitrant and abundant proteins on Earth, constitutes a challenging and underutilized material for the poultry industry. Although it resists degradation by most commonly available enzymes, natural breakdown occurs through the action of certain fungi and bacteria. This process remains poorly understood, and only a few thermophilic and anaerobic bacteria are known to effectively degrade keratin.

UV-C and hydration state drive pulsed light-induced proteome damage in spores.

Introduction: Pulsed light (PL) is a non-thermal processing technology that inactivates microorganisms through high-intensity pulses of polychromatic light, including ultraviolet-C (UV-C). While the germicidal effect of PL has been widely studied, its impact on microbial proteomes remains poorly understood. Here, we investigate the proteomic response of DSM492 (ATCC 27142) spores to PL treatment, comparing it to conventional UV-C 254 nm exposure.

Novel model organisms and proteomics for a better biological understanding.

The concept of « model organisms » is being revisited in the light of the latest advances in multi-omics technologies that can now capture the full range of molecular events that occur over time, regardless of the organism studied. Classic, well-studied models, such as Escherichia coli, Saccharomyces cerevisiae, to name a few, have long been valuable for hypothesis testing, reproducibility, and sharing common platforms among researchers. However, they are not suitable for all types of research.

Participation of gut microbiota and bacterial translocation in chronic systemic inflammation in recently diagnosed rheumatoid arthritis patients.

The objective of this study was to investigate the link between gut microbiota (GM) dysbiosis, gut inflammation, and bacterial translocation (BT) in recently diagnosed rheumatoid arthritis (RA). This case-control, observational study prospectively recruited recently diagnosed (<12 months) RA patients and age-matched healthy controls (HC) from two French hospitals between July 2014 to March 2018. The primary objective was to investigate GM composition in each group using 16S rRNA sequencing and metaproteomics approaches.

The dawn of the revolution that will allow us to precisely describe how microbiomes function.

The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins.

Proteomic profiling of the serological response to a chemically-inactivated nodavirus vaccine in European sea bass Dicentrarchus labrax.

The analysis of animal responses to immunization is fundamental to vaccine development, enabling the evaluation of immune responses and the elucidation of key mechanisms underlying protective immunity. Such insights are essential for advancing vaccines through clinical trial stages and regulatory approval. Furthermore, understanding the molecular signatures of approved vaccines not only deepens our knowledge of their function but also guides the rational design and improvement of future vaccines.

Exoproteomic Evidence for BcTSPO-Mediated Regulation of Virulence Factors in Bacillus cereus.

Bacillus cereus translocator protein (BcTSPO) is a transmembrane protein that plays a regulatory role in various Bacillus cereus phenotypes, potentially including its virulence. Given that the exoproteome is a major determinant of B. cereus virulence, particularly during the late stages of active growth, its analysis is crucial for understanding the regulatory functions of BcTSPO.

Bjerkandera adusta TM11 for the bioremediation of fluoroquinolone antibiotics spiked in wastewater: A sustainable approach to pharmaceutical contaminant biotransformation.

Global antibiotic consumption is increasing dramatically. Antibiotic release into the environment, primarily through wastewater discharge, has serious impacts for human and animal health and microbial ecosystems. To address this issue, white-rot fungi present a promising solution, as they possess oxidative enzymes that can degrade these pollutants.

Infection Reinforces the Defense Reactions in - Roots to the Detriment of Nodules.

, able to establish symbiosis with mutualistic bacteria of the genus , is one of the main species in European riparian environments, where it performs numerous biological and socioeconomic functions. However, riparian ecosystems face a growing threat from , a highly aggressive waterborne pathogen causing severe dieback in . To date, the tripartite interaction between the host plant, the symbiont , and the pathogen remains unexplored but is critical for understanding how pathogen-induced stress influences the nodule molecular machinery and thus the host-symbiont metabolism.

Cranio-facial trauma diagnosis using paleo-proteotyping of a blood sample from Robespierre (1794).

Tradition has it that the politician Robespierre, a famous tribune of the French Revolution, was lying, wounded in the face by a bullet from a firearm, on an 18th century desk, and left a trace of blood there, before being guillotined the next day (1794). This piece of furniture is now kept in the National Archives (Paris, France). A paleo-proteomic study was carried out on several brown stains on the leather of the desk, which confirmed the human blood nature of the sample, but also identified the protein signature of different cranio-facial organs.

Sample Preparation and Processing for Quick, Universal, and Insightful Microbial Proteomics.

Next-generation shotgun proteomics is one of the most valuable tools for gaining insight into the function of organisms. By providing a list of peptides and abundance information, proteomics enables the identification of proteins, their quantities, posttranslational modifications, and localization. The most refined shotgun proteomics workflow involves protein extraction, trypsin digestion, ultrahigh-performance liquid chromatography coupled to high-resolution tandem mass spectrometry, and confident assignment of resulting spectra to peptide sequences.