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Nature Communications Jul 2024Diatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The...
Diatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The identities and operational mechanisms of regulatory factors governing diatom acclimation to high light stress remain largely elusive. Here, we identified the AUREO1c protein from the coastal diatom Phaeodactylum tricornutum as a crucial regulator of non-photochemical quenching (NPQ), a photoprotective mechanism that dissipates excess energy as heat. AUREO1c detects light stress using a light-oxygen-voltage (LOV) domain and directly activates the expression of target genes, including LI818 genes that encode NPQ effector proteins, via its bZIP DNA-binding domain. In comparison to a kinase-mediated pathway reported in the freshwater green alga Chlamydomonas reinhardtii, the AUREO1c pathway exhibits a faster response and enables accumulation of LI818 transcript and protein levels to comparable degrees between continuous high-light and fluctuating-light treatments. We propose that the AUREO1c-LI818 pathway contributes to the resilience of diatoms under dynamic light conditions.
Topics: Diatoms; Light; Acclimatization; Chlamydomonas reinhardtii; Algal Proteins; Gene Expression Regulation
PubMed: 38956103
DOI: 10.1038/s41467-024-49991-7 -
Brazilian Journal of Microbiology :... Jul 2024Staphylococcus pseudintermedius, which is part of the skin microbiome of dogs, causes a variety of opportunistic infections. These infections may become more difficult...
Staphylococcus pseudintermedius, which is part of the skin microbiome of dogs, causes a variety of opportunistic infections. These infections may become more difficult to treat due to the formation of biofilm. The capacity of S. pseudintermedius to form biofilm, as well as the associated genes, has not been elucidated. This study evaluated the production and composition of S. pseudintermedius biofilm. Samples were collected from both infected dogs and asymptomatic dogs. Isolates were identified using mass spectrometry and Multiplex-PCR. Biofilm production and composition were assessed using a quantitative microtiter plate assay. The presence of ica operon genes and sps genes was investigated using conventional PCR. The investigation of Agr type and virulence genes was conducted in silico on 24 sequenced samples. All strains could produce strong biofilms, with most of the isolates presenting a polysaccharide biofilm. 63.6% of the isolates carried the complete ica operon (ADBC). All samples showed the presence of the genes spsK, spsA, and spsL, while the distribution of other genes varied. Agr type III was the most prevalent (52.2%). All sequenced samples carried the cytotoxins hlb, luk-S, luk-F, as well as the exfoliative toxins siet and se_int. No isolate displayed other exfoliative toxins. Only LB1733 presented a set of different enterotoxins (sea, seb, sec_canine, seh, sek, sel, and seq). Our findings suggest that S. pseudintermedius is a strong producer of biofilm and carries virulence genes.
PubMed: 38955982
DOI: 10.1007/s42770-024-01405-y -
Metabolomics : Official Journal of the... Jul 2024Congenital heart disease (CHD) is the most common congenital anomaly, representing a significant global disease burden. Limitations exist in our understanding of... (Observational Study)
Observational Study
INTRODUCTION
Congenital heart disease (CHD) is the most common congenital anomaly, representing a significant global disease burden. Limitations exist in our understanding of aetiology, diagnostic methodology and screening, with metabolomics offering promise in addressing these.
OBJECTIVE
To evaluate maternal metabolomics and lipidomics in prediction and risk factor identification for childhood CHD.
METHODS
We performed an observational study in mothers of children with CHD following pregnancy, using untargeted plasma metabolomics and lipidomics by ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). 190 cases (157 mothers of children with structural CHD (sCHD); 33 mothers of children with genetic CHD (gCHD)) from the children OMACp cohort and 162 controls from the ALSPAC cohort were analysed. CHD diagnoses were stratified by severity and clinical classifications. Univariate, exploratory and supervised chemometric methods were used to identify metabolites and lipids distinguishing cases and controls, alongside predictive modelling.
RESULTS
499 metabolites and lipids were annotated and used to build PLS-DA and SO-CovSel-LDA predictive models to accurately distinguish sCHD and control groups. The best performing model had an sCHD test set mean accuracy of 94.74% (sCHD test group sensitivity 93.33%; specificity 96.00%) utilising only 11 analytes. Similar test performances were seen for gCHD. Across best performing models, 37 analytes contributed to performance including amino acids, lipids, and nucleotides.
CONCLUSIONS
Here, maternal metabolomic and lipidomic analysis has facilitated the development of sensitive risk prediction models classifying mothers of children with CHD. Metabolites and lipids identified offer promise for maternal risk factor profiling, and understanding of CHD pathogenesis in the future.
Topics: Humans; Heart Defects, Congenital; Female; Metabolomics; Mothers; Lipidomics; Adult; Child; Lipids; Chromatography, High Pressure Liquid; Metabolome; Male; Pregnancy; Mass Spectrometry
PubMed: 38955892
DOI: 10.1007/s11306-024-02129-8 -
Current Microbiology Jul 2024Antimicrobial resistance is a global health issue, in which microorganisms develop resistance to antimicrobial drugs, making infections more difficult to treat. This...
Antimicrobial resistance is a global health issue, in which microorganisms develop resistance to antimicrobial drugs, making infections more difficult to treat. This threatens the effectiveness of standard medical treatments and necessitates the urgent development of new strategies to combat resistant microbes. Studies have increasingly explored natural sources of new antimicrobial agents that harness the rich diversity of compounds found in plant species. This pursuit holds promise for the discovery of novel treatments for combating antimicrobial resistance. In this context, the chemical composition, antibacterial, and antibiofilm activities of the essential oil from Croton urticifolius Lam. leaves (CuEO) were evaluated. CuEO was extracted via hydrodistillation, and its chemical constituents were identified via gas chromatography-mass spectrometry (GC/MS). The antibacterial activity of CuEO was evaluated in a 96-well plate via the microdilution method, and the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values were determined. The effect of CuEO on biofilm formation was assessed by quantifying the biomass using crystal violet staining and viable cell counting. In addition, alterations in the cellular morphology of biofilms treated with CuEO were examined using scanning electron microscopy (SEM) and laser confocal microscopy. GC/MS analysis identified 26 compounds, with elemicine (39.72%); eucalyptol (19.03%), E-caryophyllene (5.36%), and methyleugenol (4.12%) as the major compounds. In terms of antibacterial activity, CuEO showed bacteriostatic effects against Staphylococcus aureus ATCC 700698, S. aureus ATCC 25923, Staphylococcus epidermidis ATCC 12228, and Escherichia coli ATCC 11303, and bactericidal activity against S. aureus ATCC 700698. In addition, CuEO significantly inhibited bacterial biofilm formation. Microscopic analysis showed that CuEO damaged the bacterial membrane by leaching out the cytoplasmic content. Therefore, the results of this study show that the essential oil of C. urticifolius may be a promising natural alternative for preventing infections caused by bacterial biofilms. This study is the first to report the antibiofilm activity of C. urticifolius essential oil.
Topics: Biofilms; Oils, Volatile; Croton; Anti-Bacterial Agents; Microbial Sensitivity Tests; Plant Leaves; Staphylococcus aureus; Gas Chromatography-Mass Spectrometry; Plant Extracts; Cell Membrane
PubMed: 38955831
DOI: 10.1007/s00284-024-03779-6 -
Current Microbiology Jul 2024Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter... (Review)
Review
Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.
Topics: Soil Microbiology; Proteomics; Metagenomics; Bacteria; Microbiota; Fungi; Soil; Computational Biology
PubMed: 38955825
DOI: 10.1007/s00284-024-03781-y -
FEMS Microbiology Ecology Jul 2024Guaymas Basin, located off the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions,...
Guaymas Basin, located off the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions, microbial substrates like short-chain fatty acids and hydrocarbons are abiotically produced from sedimentary organic matter at comparatively shallow depths. We analyzed the effect of hydrocarbons on uptake of hydrocarbons by microorganisms via nanoscale secondary ion mass spectrometry (NanoSIMS) and microbial sulfate reduction rates (SRR), using samples from two drill sites sampled by IODP Exp. 385 (U1545C and U1546D). These sites are in close proximity of each other (ca. 1 km) and have very similar sedimentology. Site U1546D experienced the intrusion of a sill that has since then thermally equilibrated with the surrounding sediment. Both sites currently have an identical geothermal gradient, despite their different thermal history. The localized heating by the sill led to thermal cracking of sedimentary organic matter and formation of potentially bioavailable organic substrates. There were low levels of hydrocarbon and nitrogen uptake in some samples from both sites, mostly in surficial samples. Hydrocarbon and methane additions stimulated SRR in near-seafloor samples from Site U1545C, while samples from Site U1546D reacted positively only on methane. Our data indicate the potential of microorganisms to metabolize hydrocarbons even in the deep subsurface of Guaymas Basin.
PubMed: 38955392
DOI: 10.1093/femsec/fiae093 -
Journal of Microbiological Methods Jun 2024Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is the first-line method for the rapid identification of most cultured...
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is the first-line method for the rapid identification of most cultured microorganisms. As for Streptomyces strains, MALDI-TOF MS identification is complicated by the characteristic incrustation of colonies in agar and the strong cell wall of Actinomycetes cells requiring the use of alternative protein extraction protocols. In this study, we developed a specific protocol to overcome these difficulties for the MALDI-TOF MS identification of Actinomycetes made on solid medium. This protocol includes incubation of colony removed from agar plate with the beta-agarase enzyme, followed by a mechanical lysis and two washes by phosphate buffer and ethanol. Twenty-four Streptomyces and two Lentzea strains isolated from Algerian desertic soils were first identified by 16S rRNA sequencing as gold standard method, rpoB gene was used as a secondary gene target when 16S rRNA did not allow species identification. In parallel the isolates were identified by using the MALDI-TOF MS protocol as reported. After the expansion of the database with the inclusion of this MSP, the strains were analyzed again in MALDI Biotyper, and all were identified. This work demonstrates that the rapid identification of Actinomycetes can be obtained without protein extraction step frequently used in MALDI-TOF mass spectrometry with this type of microorganisms.
PubMed: 38955305
DOI: 10.1016/j.mimet.2024.106984 -
International Journal of Biological... Jun 2024The global pandemic caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had profoundly detrimental effects on our society....
The global pandemic caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had profoundly detrimental effects on our society. To combat this highly pathogenic virus, we turned our attention to an abundant renewable natural aromatic polymer found in wood. Through a chemical modification of Eucalyptus and Japanese cedar wood via acidic microwave solvolysis in equivolume mixture of 2 % (w/w) aqueous HSO, ethylene glycol, and toluene at 190 °C. Subsequently, we separated the resulting solvolysis products through extractions with toluene, ethyl acetate, and ethanol. Among these products, the ethyl acetate extract from Eucalyptus wood (eEAE) demonstrated the highest inhibition effects against the novel SARS-CoV-2. We further divided eEAE into four fractions, and a hexane extract from the ethanol-soluble portion, termed eEAE3, exhibited the most substantial inhibitory rate at 93.0 % when tested at a concentration of 0.5 mg/mL. Analyzing eEAE3 using pyrolysis gas chromatography-mass spectrometry revealed that its primary components are derived from lignin. Additionally, HC edited-heteronuclear single quantum coherence nuclear magnetic resonance analysis showed that the solvolysis process cleaved major lignin interunit linkages. Considering the abundance and renewability of lignin, the lignin-derived anti-SARS-CoV-2 agent presents a promising potential for application in suppressing infections within our everyday environment.
PubMed: 38955295
DOI: 10.1016/j.ijbiomac.2024.133556 -
Journal of Pharmacological and... Jun 2024Quantification of the unbound portion of platinum (Pt) in human plasma is important for assessing the pharmacokinetics of the chemotherapeutic drug cisplatin. In this...
Quantification of the unbound portion of platinum (Pt) in human plasma is important for assessing the pharmacokinetics of the chemotherapeutic drug cisplatin. In this study, we sought to compare the recovery of unbound Pt using Nanosep® filters to 1) traditional filters (Centrifree®, Centrisart®, Amicon®) or trichloroacetic acid (TCA) protein precipitation, and 2) unbound, bound, and total Pt concentrations in clinical specimens. For the tested filters, the impact of 1) molecular weight cut-offs, 2) centrifugation force, and 3) total Pt concentration on Pt binding in human plasma was evaluated. Pt was quantified using inductively coupled-plasma mass spectrometry. In human plasma spiked with 0.9 μg/mL Pt, the percent of unbound Pt increased at higher centrifugation speeds. By comparison, the percent of unbound Pt was highest (42.1%) following TCA protein precipitation. When total Pt was ≤0.9 μg/mL, unbound Pt (~20-30%) was consistent across filters. Conversely, when plasma was spiked with Pt exceeding 0.9 μg/mL, the percent of unbound Pt increased from 36.5 to 48% using ultrafiltration, compared to 63.4% to 79% with TCA precipitation. In patients receiving cisplatin-containing chemotherapy, the fraction of unbound Pt at concentrations exceeding 0.9 μg/mL ranged between 35 and 90%. Moreover, the unbound fraction of Pt in plasma correlated with the concentration of unbound (R = 0.738) and total Pt (R = 0.335). In summary, this study demonstrates that 1) the percent of unbound Pt is influenced by total and unbound Pt levels in vitro and in clinical specimens, and 2) ultrafiltration with Nanosep® filters is a feasible method for quantifying unbound Pt concentrations in human plasma.
PubMed: 38955285
DOI: 10.1016/j.vascn.2024.107535 -
The Science of the Total Environment Jun 2024In this study, a comprehensive and sensitive method for the simultaneous detection of 17 opioids (OPs) and their human metabolites in wastewater using high-performance...
In this study, a comprehensive and sensitive method for the simultaneous detection of 17 opioids (OPs) and their human metabolites in wastewater using high-performance liquid chromatography coupled to tandem mass spectrometry was validated. The chromatographic separations of opioids were carried out on a Kinetex® Biphenyl column (1.7 μm, 100 Å, 50 × 2.1 mm). A synthetic wastewater approach was used for recovery studies to mimic a contaminant-free matrix. Two solid-phase extraction (SPE) sorbents (hydrophilic-lipophilic balance and mixed mode with the previous phase and a weak cationic exchange) were studied to optimize sample treatment and obtain higher recoveries. The mixed mode was chosen because the recoveries of 17 target analytes at three spiked concentrations (25, 50, and 100 ng/ml) were > 80 % for 75 % of the analytes in a simulated wastewater. The intra- and inter-day relative standard deviations (RSDs) were between ±1 % and ±20 %. The method limits of quantification ranged from 5 to 25 ng L, the only exceptions being heroin (275 ng L) and morphine-3β-glucuronide (250 ng L). Suppression/enhancement is comparable between the synthetic and the influent wastewater. The analytical method was applied to the OPs analysis in twenty-one influent samples collected from the treatment plants treating the wastewater of Valencia City (Spain). Twelve OPs were detected with total daily concentrations ranging from 1 ng L to 2135 ng L. The widespread presence of these compounds in water suggests potential widespread exposure, highlighting the need for increased environmental awareness. Furthermore, the estimated daily intake results raise concerns about opioid use as a potential future health and social issue.
PubMed: 38955278
DOI: 10.1016/j.scitotenv.2024.174382