The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes

BACKGROUND

By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems.

RESULTS

Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to optimally exploit extensive tandem mass spectrometry data. This approach leverages the capabilities of the first generation of Quadrupole Orbitrap mass spectrometer incorporating an asymmetric track lossless (Astral) analyzer, offering rapid MS/MS scan speed and sensitivity. We took advantage of data-dependent acquisition and data-independent acquisition strategies using a peptide extract from a human fecal sample spiked with precise amounts of peptides from two reference bacteria.

CONCLUSIONS

Our approach, which combines both acquisition methods, proves to be time-efficient while processing extensive generic databases and massive datasets, achieving a coverage of more than 122,000 unique peptides and 38,000 protein groups within a 30-min DIA run. This marks a significant departure from current state-of-the-art metaproteomics methodologies, resulting in broader coverage of the metabolic pathways governing the biological system. In combination, our strategy and the Astral mass analyzer represent a quantum leap in the functional analysis of microbiomes. Video Abstract.

Mixture effects of pharmaceuticals carbamazepine, diclofenac and venlafaxine on Mytilus galloprovincialis mussel probed by metabolomics and proteogenomics combined approach

Exposure to single molecules under laboratory conditions has led to a better understanding of the mechanisms of action (MeOAs) and effects of pharmaceutical active compounds (PhACs) on non-target organisms. However, not taking the co-occurrence of contaminants in the environment and their possible interactions into account may lead to underestimation of their impacts. In this study, we combined untargeted metabolomics and proteogenomics approaches to assess the mixture effects of diclofenac, carbamazepine and venlafaxine on marine mussels (Mytilus galloprovincialis). Our multi-omics approach and data fusion strategy highlighted how such xenobiotic cocktails induce important cellular changes that can be harmful to marine bivalves. This response is mainly characterized by energy metabolism disruption, fatty acid degradation, protein synthesis and degradation, and the induction of endoplasmic reticulum stress and oxidative stress. The known MeOAs and molecular signatures of PhACs were taken into consideration to gain insight into the mixture effects, thereby revealing a potential additive effect. Multi-omics approaches on mussels as sentinels offer a comprehensive overview of molecular and cellular responses triggered by exposure to contaminant mixtures, even at environmental concentrations.

Liquid chromatography-mass spectrometry based metabolomics investigation of different tissues of Mytilus galloprovincialis

The Mediterranean mussel (Mytilus galloprovincialis) is widely used in monitoring programs and in ecotoxicological studies to examine the biological effects of physicochemical parameter changes and the impact of chemical pollutants. Metabolomics has recently demonstrated high potential to gain further insight into the molecular effects of chemical exposure and the success of its application is dependent on the extent of prior metabolomics knowledge available on the target organism. Therefore, the purpose of this study was the investigation of the metabolites of five different functional tissues of male and female Mediterranean mussels (digestive gland, foot, gill and gonad tissues and in the remaining soft tissues) accessible to the analysis using the most common sample preparation recommended for tissue analysis (i.e. Bligh & Dyer). Metabolic fingerprints were acquired via liquid chromatography high-resolution mass spectrometry and the identification was based on an internal database developed in the laboratory. It led to the identification of 110 metabolites, among which amino acids, carboxylic acids, purine and pyrimidine metabolites were often the most abundant. The metabolic contents of the five tissues quantitatively and qualitatively differed, with a clear distinction between male and female contents observed in the gonads and digestive glands. These results underline the importance of selecting the most suitable tissue and sex to study the impact of contamination on metabolism and the need for further research to deeper characterize the metabolome of this organism.

Early Biological Modulations Resulting from 1-Week Venlafaxine Exposure of Marine Mussels Mytilus galloprovincialis Determined by a Metabolomic Approach

There is growing evidence of the presence of pharmaceuticals in natural waters and their accumulation in aquatic organisms. While their mode of action on non-target organisms is still not clearly understood, their effects warrant assessment. The present study assessed the metabolome of the Mediterranean mussel (Mytilus galloprovincialis) exposed to a 10 µg/L nominal concentration of the antidepressant venlafaxine (VLF) at 3 time-points (1, 3, and 7 days). Over the exposure period, we observed up- or down-modulations of 113 metabolites, belonging to several metabolisms, e.g., amino acids (phenylalanine, tyrosine, tryptophan, etc.), purine and pyrimidine metabolisms (adenosine, cyclic AMP, thymidine, etc.), and several other metabolites involved in diverse functions. Serotonin showed the same time-course modulation pattern in both male and female mussels, which was consistent with its mode of action in humans, i.e., after a slight decrease on the first day of exposure, its levels increased at day 7 in exposed mussels. We found that the modulation pattern of impacted metabolites was not constant over time and it was gender-specific, as male and female mussels responded differently to VLF exposure.

Environmental Metabolomics Promises and Achievements in the Field of Aquatic Ecotoxicology: Viewed through the Pharmaceutical Lens

Scientists often set ambitious targets using environmental metabolomics to address challenging ecotoxicological issues. This promising approach has a high potential to elucidate the mechanisms of action (MeOAs) of contaminants (in hazard assessments) and to develop biomarkers (in environmental biomonitoring). However, metabolomics fingerprints often involve a complex mixture of molecular effects that are hard to link to a specific MeOA (if detected in the analytical conditions used). Given these promises and limitations, here we propose an updated review on the achievements of this approach. Metabolomics-based studies conducted on the effects of pharmaceutical active compounds in aquatic organisms provide a relevant means to review the achievements of this approach, as prior knowledge about the MeOA of these molecules could help overcome some shortcomings. This review highlighted that current metabolomics advances have enabled more accurate MeOA assessment, especially when combined with other omics approaches. The combination of metabolomics with other measured biological endpoints has also turned out to be an efficient way to link molecular effects to (sub)-individual adverse outcomes, thereby paving the way to the construction of adverse outcome pathways (AOPs). Here, we also discuss the importance of determining MeOA as a key strategy in the identification of MeOA-specific biomarkers for biomonitoring. We have put forward some recommendations to take full advantage of environmental metabolomics and thus help fulfil these promises.

An integrated metabolomics and proteogenomics approach reveals molecular alterations following carbamazepine exposure in the male mussel Mytilus galloprovincialis

Carbamazepine is one of the most abundant pharmaceutical active compounds detected in aquatic systems. Based on laboratory exposures, carbamazepine has been proven to adversely affect aquatic organisms. However, the underlying molecular events remain poorly understood. This study aims to investigate the molecular mechanisms potentially associated with toxicological effects of carbamazepine on the mussel Mytilus galloprovincialis exposed for 3 days at realistic concentrations encountered in coastal environments (80 ng/L and 8 μg/L). An integrated metabolomics and proteogenomics approach, including data fusion strategy, was applied to gain more insight in molecular events and cellular processes triggered by carbamazepine exposure. Consistent metabolic and protein signatures revealed a metabolic rewiring and cellular stress at both concentrations (e.g. intensification of protein synthesis, transport and catabolism processes, disruption of lipid and amino acid metabolisms). These highlighted molecular signatures point to the induction of autophagy, closely related with carbamazepine mechanism of action, as well as a destabilization of the lysosomal membranes and an enzymatic overactivity of the peroxisomes. Induction of programmed cell death was highlighted by the modulation of apoptotic cognate proteins. The proposed integrative omics data analysis was shown to be highly relevant to identify the modulations of the two molecular levels, i.e. metabolites and proteins. Multi-omics approach is able to explain the resulting complex biological system, and document stronger toxicological pieces of evidence on pharmaceutical active compounds at environmental concentrations in sentinel organisms.

Elucidating venlafaxine metabolism in the Mediterranean mussel (Mytilus galloprovincialis) through combined targeted and non-targeted approaches

Exposure of aquatic organisms to antidepressants is currently well documented, while little information is available on how wild organisms cope with exposure to these pharmaceutical products. Studies on antidepressant metabolism in exposed organisms could generate information on their detoxification pathways and pharmacokinetics. The goal of this study was to enhance knowledge on the metabolism of venlafaxine (VEN)-an antidepressant frequently found in aquatic ecosystems-in Mytilus galloprovincialis, a bivalve that is present worldwide. An original tissue extraction technique based on the cationic properties of VEN was developed for further analysis of VEN and its metabolites using targeted and non-targeted approaches. This extraction method was assessed in terms of recovery and matrix effects for VEN metabolites. Commercial analytical standards were applied to characterize metabolites found in mussels exposed to 10 μg/L VEN for 3 and 7 days. Targeted and non-targeted approaches using liquid chromatography (LC) combined with high-resolution mass spectrometry (HRMS) were implemented to screen for expected metabolites based on the literature on aquatic species, and for metabolites not previously documented. Four venlafaxine metabolites were identified, namely N-desmethylvenlafaxine and O-desmethylvenlafaxine, which were clearly identified using analytical standards, and two other metabolites revealed by non-target analysis. According to the signal intensity, hydroxy-venlafaxine (OH-VEN) was the predominant metabolite detected in mussels exposed for 3 and 7 days.

Metabolomics approach reveals disruption of metabolic pathways in the marine bivalve Mytilus galloprovincialis exposed to a WWTP effluent extract

Conventional wastewater treatment plants (WWTPs) discharge a highly diverse range of organic contaminants in aquatic environments, including marine waters. The health of marine ecosystems could be threatened by contaminants release. Environmental metabolomics can be helpful to assess the effects of multi-contamination on marine organisms without any a priori information since it is able to provide meaningful information on the biochemical response of organisms to a stress. The aim of the present study was to evaluate the potential of metabolomics to highlight key metabolites disrupted by a WWTP effluent extract exposure and then elucidate the biological effects of such exposure on Mediterranean mussels (Mytilus galloprovincialis). Exposed male mussels showed numerous metabolites altered in response to WWTP effluent exposure. The highlighted metabolites belong mainly to amino acids metabolism (e.g. tyrosine, phenylalanine, leucine, proline, etc.), neurohormones (dopamine and a serotonin metabolite), purine and pyrimidine metabolism (e.g. adenosine, adenine, guanine, uracil etc.), citric acid cycle intermediates (e.g. malate, fumarate), and a component involved in oxidative stress defense (oxidized glutathione). Modulation of these metabolites could reflect the alteration of several biological processes such as energy metabolism, DNA and RNA synthesis, immune system, osmoregulation, byssus formation and reproduction, which may lead to a negative impact of organism fitness. Our study provided further insight into the effects of WWTP effluents on marine organisms.

Gene expression profiles associated with survival of individual rat dentate cells after endogenous corticosteroid deprivation

Removal of circulating corticosterone by adrenalectomy (ADX) leads to apoptosis after 3 days in a small population of rat dentate granule neurons, whereas most surrounding cells remain viable. Interestingly, a specific expression profile is triggered in surviving granule cells that may enhance their survival. Hippocampal slices prepared 1, 2 or 3 days after ADX or sham operation were stained ex vivo with Hoechst 33258, which serves to identify apoptotic neurons. After electrophysiological analysis, multiple gene expression in surviving individual granule cells was assessed by linear antisense RNA amplification and hybridization to slot blots containing various neuronal cDNAs. Hierarchical clustering and principal component analysis was performed on two physiological variables and 14 mRNA ratios from ADX cells from every time point. Our results indicate that surviving 3-day ADX granule cells display lower membrane capacitance, lower relative N-methyl-d-aspartate (NMDA) R1 mRNA expression and higher relative mineralocorticoid receptor (MR), alpha1A voltage-gated Ca-channel, Bcl-2 and NMDA R2C mRNA expression. Some 1- and 2-day ADX cells cluster with these 3-day survivors; therefore, one or more components of their mRNA expression profile may represent predictive markers for apoptosis resistance. The functional relevance of two candidate genes was tested by in vivo local over-expression in the same model system; of these, Bcl-2 conferred partial protection when induced shortly before ADX. Therefore, removal of corticosteroids triggers a specific gene expression profile in surviving dentate granule cells; key components of this profile may be associated with their survival.

Sexual behavior of stallions during in-hand natural service and semen collection: an observation in French studs

The sexual behavior of 42 stallions from French national and private studs was examined in two contexts: semen collection for artificial insemination (AI) and in-hand natural service (NS). Each stallion was observed twice in the same context. Erection and ejaculation latencies, the number of mounts leading to ejaculation, dismount latency and total breeding time were measured and compared between AI and NS. Mount without erection was rare (6/83 observations). Erection latency was 89+/-11s, and was not different between NS (62+/-22s) and AI (100+/-13s, P=0.128). Stallions ejaculated after either one mount (62/83 observations), or two (11/83 observations) or three mounts (10/83 observations). Ejaculation latency was 85+/-15s (84+/-19 in AI and 86+/-28 in NS). If 1st mount did not lead to ejaculation, then ejaculation latency increased several fold following the 2nd mount during both AI and NS. The results provide reference measures for semen collection in French studs. Difference in erection latency between AI and NS, although not statistically significant, may reflect different contributions of excitatory inputs from the brain and the genital area to the activation of spinal networks controlling erection. In contrast, lack of difference in ejaculation latency between AI and NS suggests that the spinal network that controls ejaculation follows a more rigid motor pattern.

Sparing of neuronal function postseizure with gene therapy

Numerous studies have demonstrated that gene therapy interventions can protect neurons from death after neurological insults. In nearly all such studies, however, "protection" consists of reduced neurotoxicity, with no demonstrated preservation of neuronal function. We used a herpes simplex virus-1 system to overexpress either the Glut-1 glucose transporter (GT) (to buffer energetics), or the apoptosis inhibitor Bcl-2. Both decreased hippocampal neuron loss to similar extents during excitotoxic insults in vitro and in vivo. However, the mediating mechanisms and consequences of the two interventions differed. GT overexpression attenuated early, energy-dependent facets of cell death, blocking oxygen radical accumulation. Bcl-2 expression, in contrast, blocked components of death downstream from the energetic and oxidative facets. Most importantly, GT- but not Bcl-2-mediated protection preserved hippocampal function as assessed spatial maze performance. Thus, gene therapeutic sparing of neurons from insult-induced death does not necessarily translate into sparing of function.

Delivery of herpes simplex virus amplicon-based vectors to the dentate gyrus does not alter hippocampal synaptic transmission in vivo

Herpes simplex virus type-1 (HSV) amplicon vectors containing neuroprotective genes can alter cell physiology and enhance survival following various insults. However, to date, little is known about effects of viral infection itself (independent of the gene delivered) on neuronal physiology. Electrically-evoked synaptic responses are routinely recorded to measure functional alterations in the nervous system and were used here to assess the potential capability of HSV vectors to disrupt physiology of the hippocampus (a forebrain structure involved in learning that is highly susceptible to necrotic insult, making it a frequent target in gene therapy research). Population excitatory post-synaptic potentials (EPSPs) were recorded in the dentate gyrus (DG) and in area CA3 in vivo 72 h after infusion of an HSV vector expressing a reporter gene (lacZ) or vehicle into the DG. Evoked perforant path (PP-DG) or mossy fiber (MF-CA3) EPSPs slope values measured across input/output (I/O) curves were not altered by infection. Paired-pulse facilitation at either recording site was also unaffected. X-gal-positive granule cells surrounded the recording electrode (PP-DG recording) and stimulating electrode tracts (MF-CA3 recording) in animals that received vector, suggesting that we had measured function, at least in part, in infected neurons. Because of the negative electrophysiological result, we sought to deliver a gene with an HSV amplicon which would affect the measured endpoints, as a positive control. Delivery of calbindin D28kpotentiated PP-DG synaptic strength, indicating that our recording system could detect alterations due to vector expression. Thus, the data indicate that HSV vectors are benign, in regard to effects on synaptic function, and support the use of these vectors as a safe method to deliver selected genes to the central nervous system.

Effect of glyphosate on ethylene production in tobacco callus

Glyphosate (N-phosphonomethylglycine) caused a significant decrease or a slight increase in ethylene production in tobacco callus (Nicotiana tabacum L.) depending on the concentration of indole-3-acetic acid (IAA) present in the medium. IAA stimulated ethylene production, but a pretreatment with glyphosate greatly reduced the IAA-induced ethylene production. Inasmuch as glyphosate treatment promoted the metabolism of IAA, the decrease in ethylene production induced by glyphosate is attributed to the rapid loss of free IAA in the treated tissue.

Microdetermination of Ethylene Dibromide in Air by Gas Chromatography

Using a new, sensitive photo-ionization detector in a portable gas chromatograph that operates at ambient temperature, a method was developed for determining ethylene dibromide in air as low as 19 ppb. Vapor standards were prepared for calibration of the detector; concentrations in these standards were accurately determined by using a flame ionization detector. This detector was previously calibrated with an aqueous standard of ethylene dibromide. Using the 2 gas chromatographs, the loss of ethylene dibromide through sorption from the atmosphere of the vapor standards was determined. Solubility of ethylene dibromide in water was also established at 3 temperatures, using the flame ionization detector.

Does ethylene mediate root growth inhibition by indole-3-acetic Acid?

The effects of ethylene and of indole-3-acetic acid (IAA) on growth of excised pea root sections have been compared under a variety of conditions. After 16 hours treatment the inhibitory action of IAA is fully reversible on transfer of the root sections to IAA-free solutions. In contrast, inhibition by ethylene is almost totally irreversible. IAA inhibits growth from zero time; ethylene is generally without effect during the first 3 to 6 hours. The inhibitory action of ethylene is dependent on factors such as tissue age and solution composition which have no major effect on IAA inhibition. Ethylene production is enhanced by 100 mum IAA, but conditions which reduce the rate of ethylene evolution 2 to 3-fold at the same IAA concentration fail to affect the inhibitory action of IAA on elongation. It seems unlikely that ethylene can play more than a minor role in mediating inhibition of pea root growth by IAA.