Application of the Hollow-Fiber Infection Model to Personalized Precision Dosing of Isoniazid in a Clinical Setting.

BACKGROUND: The hollow-fiber infection model (HFIM) is a valuable tool for evaluating pharmacokinetics/pharmacodynamics relationships and determining the optimal antibiotic dose in monotherapy or combination therapy, but the application for personalized precision medicine in tuberculosis treatment remains limited. This study aimed to evaluate the efficacy of adjusted antibiotic doses for a tuberculosis patient using HFIM. METHODS: Model-based Bayesian forecasting was utilized to assess the proposed reduction of the isoniazid dose from 300 mg daily to 150 mg daily in a patient with an ultra-slow-acetylation phenotype. The efficacy of the adjusted 150-mg dose was evaluated in a time-to-kill assay performed using the bacterial isolate Mycobacterium tuberculosis (Mtb) H37Ra in a HFIM that mimicked the individual pharmacokinetic profile of the patient. RESULTS: The isoniazid concentration observed in the HFIM adequately reflected the target drug exposures simulated by the model. After 7 days of repeated dose administration, isoniazid killed 4 log10 Mtb CFU/mL in the treatment arm, while the control arm without isoniazid increased 1.6 log10 CFU/mL. CONCLUSION: Our results provide an example of the utility of the HFIM for predicting the efficacy of specific recommended doses of anti-tuberculosis drugs in real clinical setting.

Enhancing Sensitivity in Gas Detection: Porous Structures in Organic Field-Effect Transistor-Based Sensors.

Gas detection is crucial for detecting environmentally harmful gases. Organic field-effect transistor (OFET)-based gas sensors have attracted attention due to their promising performance and potential for integration into flexible and wearable devices. This review examines the operating mechanisms of OFET-based gas sensors and explores methods for improving sensitivity, with a focus on porous structures. Researchers have achieved significant enhancements in sensor performance by controlling the thickness and free volume of the organic semiconductor layer. Additionally, innovative fabrication techniques like self-assembly and etching have been used to create porous structures, facilitating the diffusion of target gas molecules, and improving sensor response and recovery. These advancements in porous structure fabrication suggest a promising future for OFET-based gas sensors, offering increased sensitivity and selectivity across various applications.

Time-course cross-species transcriptomics reveals conserved hepatotoxicity pathways induced by repeated administration of cyclosporine A.

Cyclosporine A (CsA) has shown efficacy against immunity-related diseases despite its toxicity in various organs, including the liver, emphasizing the need to elucidate its underlying hepatotoxicity mechanism. This study aimed to capture the alterations in genome-wide expression over time and the subsequent perturbations of corresponding pathways across species. Six data from humans, mice, and rats, including animal liver tissue, human liver microtissues, and two liver cell lines exposed to CsA toxic dose, were used. The microtissue exposed to CsA for 10 d was analyzed to obtain dynamically differentially expressed genes (DEGs). Single-time points data at 1, 3, 5, 7, and 28 d of different species were used to provide additional evidence. Using liver microtissue-based longitudinal design, DEGs that were consistently up- or down-regulated over time were captured, and the well-known mechanism involved in CsA toxicity was elucidated. Thirty DEGs that consistently changed in longitudinal data were also altered in 28-d rat in-house data with concordant expression. Some genes (e.g. TUBB2A, PLIN2, APOB) showed good concordance with identified DEGs in 1-d and 7-d mouse data. Pathway analysis revealed up-regulations of protein processing, asparagine N-linked glycosylation, and cargo concentration in the endoplasmic reticulum. Furthermore, the down-regulations of pathways related to biological oxidations and metabolite and lipid metabolism were elucidated. These pathways were also enriched in single-time-point data and conserved across species, implying their biological significance and generalizability. Overall, the human organoids-based longitudinal design coupled with cross-species validation provides temporal molecular change tracking, aiding mechanistic elucidation and biologically relevant biomarker discovery.

Pathway-level multi-omics analysis of the molecular mechanisms underlying the toxicity of long-term tacrolimus exposure.

Tacrolimus (TAC)-based treatment is associated with nephrotoxicity and hepatotoxicity; however, the underlying molecular mechanisms responsible for this toxicity have not been fully explored. This study elucidated the molecular processes underlying the toxic effects of TAC using an integrative omics approach. Rats were sacrificed after 4 weeks of daily oral TAC administration at a dose of 5 mg/kg. The liver and kidney underwent genome-wide gene expression profiling and untargeted metabolomics assays. Molecular alterations were identified using individual data profiling modalities and further characterized by pathway-level transcriptomics-metabolomics integration analysis. Metabolic disturbances were mainly related to an imbalance in oxidant-antioxidant status, as well as in lipid and amino acid metabolism in the liver and kidney. Gene expression profiles also indicated profound molecular alterations, including in genes associated with a dysregulated immune response, proinflammatory signals, and programmed cell death in the liver and kidney. Joint-pathway analysis indicated that the toxicity of TAC was associated with DNA synthesis disruption, oxidative stress, and cell membrane permeabilization, as well as lipid and glucose metabolism. In conclusion, our pathway-level integration of transcriptome and metabolome and conventional analyses of individual omics profiles, provided a more comprehensive picture of the molecular changes resulting from TAC toxicity. This study also serves as a valuable resource for subsequent investigations aiming to understand the mechanism underlying the molecular toxicology of TAC.

Multi-Redox Responsive Behavior in a Mixed-Valence Semiconducting Framework Based on Bis-[1,2,5]-thiadiazolo-tetracyanoquinodimethane.

The two-dimensional (2-D) framework, [Cu(BTDAT)(MeOH)] {BTDAT = bis-[1,2,5]-thiadiazolo-tetracyanoquinodimethane}, possesses remarkable multi-step redox properties, with electrochemical studies revealing six quasi-stable redox states in the solid state. In situ electron paramagnetic resonance and visible-near infrared spectroelectrochemistry elucidated the mechanism for these multi-step redox processes, as well as the optical and electrochromic behavior of the BTDAT ligand and framework. In studying the structural, spectroscopic, and electronic properties of [Cu(BTDAT)(MeOH)], the as-synthesized framework was found to exist in a mixed-valence state with thermally-activated semiconducting behavior. In addition to pressed pellet conductivity measurements, single-crystal conductivity measurements using a pre-patterned polydimethylsiloxane layer on a silicon substrate provide important insights into the anisotropic conduction pathways. As an avenue to further understand the electronic state of [Cu(BTDAT)(MeOH)], computational band structure calculations predicted delocalized electronic transport in the framework. On the balance of probabilities, we propose that [Cu(BTDAT)(MeOH)] is a Mott insulator (i.e., electron correlations cause a metal-insulator transition). This implies that the conductivity is incoherent. However, we are unable to distinguish between activated transport due to Coulombically bound electron-hole pairs and a hopping mechanism. The combined electrochemical, electronic, and optical properties of [Cu(BTDAT)(MeOH)] shine a new light on the experimental and theoretical challenges for electroactive framework materials, which are implicated as the basis of advanced optoelectronic and electrochromic devices.

Delineation of the molecular mechanisms underlying Colistin-mediated toxicity using metabolomic and transcriptomic analyses.

The mechanisms underlying colistin-induced toxicity are not fully understood. This study used untargeted metabolomics and transcriptomics to elucidate the molecular processes occurring in the liver and kidney of rats after treatment with colistin methanesulfonate (CMS). Rats were treated with 50 mg/kg CMS (high-dose), 25 mg/kg CMS (low-dose), or vehicle control, either as a single dose or once daily for 1 or 4 weeks. We found that metabolic alterations were dose- and treatment duration-dependent in the kidney, whereas mild changes were noted in the liver. Metabolic profiles in the high-dose, low-dose, and control groups of both tissues could be classified using partial least-squares discriminant analysis. Metabolic alterations were associated with the citric acid cycle and related processes, disrupted balance between pro-oxidants and antioxidants, inflammatory responses, and amino acid and nucleic acid metabolism. Gene expression profiles further showed that high-dose treatment was associated with disrupted metabolism, oxidative stress, and proinflammatory signals in the kidney. The expression levels of genes related to the cell cycle, DNA replication, and programmed cell death were also predominantly upregulated. These findings suggested that high-dose treatment was associated with a dramatic increase in cellular kidney injury, while only minor effects were observed in the low-dose group. Almost no significant gene expression was changed in the liver, even with high-dose CMS. In conclusion, untargeted metabolomics and transcriptomics provided better insights into the biological mechanisms underlying colistin-induced nephrotoxicity.

Systematic in situ hydration neutron reflectometry study on Nafion thin films.

Reported herein is a neutron reflectometry (NR) study on hydrated Nafion thin films (∼30 nm) on a silicon substrate with native oxide. The Nafion morphology is investigated systematically across the whole relative humidity range using both H2O and D2O vapours to enable a comparative study. By utilising this systematic approach two key results have been obtained. The first is that by leveraging the strong positive scattering signal from the D2O vapour, a complete and systematic water adsorption isotherm (Type II) for a Nafion thin film is produced. Utilising the slight negative scattering signal of the H2O enabled the quantification of the hydration dependent evolution of the formation of Nafion/water lamellae near the substrate surface. The number of lamellae layers increases continuously with hydration, and does not form abruptly. We also report the effects of swelling on the thin films across the relative humidity ranges. The work reported should prove useful in quantifying other hydration dependent properties of Nafion thin films such as conductivity and understanding Nafion/semiconductor based devices, as well as showcasing a NR methodology for other hydrophilic polymers.

Student generation and peer review of examination questions in the dental curriculum: Enhancing student engagement and learning.

BACKGROUND: Writing, sharing, answering, discussing and rating examination questions are a way to involve students in creating content and applying their knowledge. The PeerWise online question-setting platform facilitates student communities in this activity. This mixed-methods study asks the question: Does students' writing and answering examination questions enhance their engagement and learning of Neurology as a Life Science topic? METHODS: Over a 2-year period, self-assembled groups of 3-4 students submitted 1-2 multiple-choice questions (MCQs) every 2 weeks into the PeerWise portal for review by their peers. Summative examination results were compared with previous year's control group. Data were also collected regarding student engagement (number of MCQs answered or submitted comments) are compared to summative assessment results at the end of semester. Post-intervention student satisfaction surveys were analysed qualitatively and quantitatively to assess the effectiveness of the exercise. RESULTS: With 174 and 80 student participants in intervention and control groups, respectively, no statistical difference was found in the average marks between the cohorts. However, within intervention group, positive correlation (Spearman's r = .272-.333) was found between higher level of student engagement with PeerWise and higher examination result. Positive correlation remained persistent after completion of the PeerWise exercise. Student survey revealed greater engagement with subject content, and qualitative thematic analysis was mapped to define various ways students engaged with the PeerWise activity. CONCLUSION: Tasking students to regularly generate and review MCQs enhances engagement with the topic, and higher engagement with PeerWise correlating to higher examination scores.

Characterization of a diet-induced obesity rat model for periodontal research.

OBJECTIVES: Obesity is associated with periodontitis, but the mechanisms underlying this association have yet to be unraveled. The present investigation was to evaluate a common rat model, in which obesity is induced by high-fat, high-sucrose diet (HFSD), for its applicability in periodontal research. MATERIALS AND METHODS: Ten male Wistar rats were fed a 3-month HFSD along with a matching control group. Afterwards, the body weight, adipocyte morphology, leptin and adiponectin levels in adipose tissue, gingiva, and serum as well as the serum levels of triglyceride, cholesterol, and glucose were analyzed. For statistical analyses, parametric and non-parametric tests were applied (p < 0.05). RESULTS: Body weight was significantly higher in the HFSD group after dieting as compared to control. HFSD caused a significant increase in serum triglyceride, low-density lipoprotein cholesterol, and leptin levels and a significant decrease in high-density lipoprotein cholesterol. Furthermore, adipose tissue from HFSD rats exhibited significantly larger adipocytes, displayed a significant upregulation of leptin and, surprisingly, elevated adiponectin levels, which is in contrast to chronic obesity in humans. Although leptin and adiponectin were also observed in gingival biopsies, no obvious differences between the groups were found. CONCLUSIONS: Although this rat diet-induced obesity model is characterized by changes typical of obesity, it also has limitations, which have to be considered when data, especially with regard to adipokines, are extrapolated to humans. CLINICAL RELEVANCE: The rodent diet-induced obesity model may be useful for unraveling pathomechanisms underlying the association between obesity and periodontal destruction but conclusions have to be drawn with caution.

Assessing the public acceptability of proposed policy interventions to reduce the misuse of antibiotics in Australia: A report on two community juries.

OBJECTIVE: To elicit the views of well-informed community members on the acceptability of proposed policy interventions designed to improve community use of antibiotics in Australia. DESIGN: Two community juries held in 2016. SETTING AND PARTICIPANTS: Western Sydney and Dubbo communities in NSW, Australia. Twenty-nine participants of diverse social and cultural backgrounds, mixed genders and ages recruited via public advertising: one jury was drawn from a large metropolitan setting; the other from a regional/rural setting. MAIN OUTCOME MEASURE: Jury verdict and rationale in response to a prioritization task and structured questions. RESULTS: Both juries concluded that potential policy interventions to curb antibiotic misuse in the community should be directed towards: (i) ensuring that the public and prescribers were better educated about the dangers of antibiotic resistance; (ii) making community-based human and animal health-care practitioners accountable for their prescribing decisions. Patient-centred approaches such as delayed prescribing were seen as less acceptable than prescriber-centred approaches; both juries completely rejected any proposal to decrease consumer demand by increasing antibiotic prices. CONCLUSION: These informed citizens acknowledged the importance of raising public awareness of the risks, impacts and costs of antibiotic resistance and placed a high priority on increasing social and professional accountability through restrictive measures. Their overarching aim was that policy interventions should be directed towards creating collective actions and broad social support for changing antibiotic use through establishing and explaining the need for mechanisms to control and support better prescribing by practitioners, while not transferring the burdens, costs and risks of interventions to consumers.

An active learning-enabled annotation system for clinical named entity recognition.

BACKGROUND: Active learning (AL) has shown the promising potential to minimize the annotation cost while maximizing the performance in building statistical natural language processing (NLP) models. However, very few studies have investigated AL in a real-life setting in medical domain. METHODS: In this study, we developed the first AL-enabled annotation system for clinical named entity recognition (NER) with a novel AL algorithm. Besides the simulation study to evaluate the novel AL algorithm, we further conducted user studies with two nurses using this system to assess the performance of AL in real world annotation processes for building clinical NER models. RESULTS: The simulation results show that the novel AL algorithm outperformed traditional AL algorithm and random sampling. However, the user study tells a different story that AL methods did not always perform better than random sampling for different users. CONCLUSIONS: We found that the increased information content of actively selected sentences is strongly offset by the increased time required to annotate them. Moreover, the annotation time was not considered in the querying algorithms. Our future work includes developing better AL algorithms with the estimation of annotation time and evaluating the system with larger number of users.

Purification and characterisation of recombinant His-tagged RgpB gingipain from Porphymonas gingivalis.

Gingipain proteases are important virulence factors from the periodontal pathogen Porphyromonas gingivalis and are the target of many in vitro studies. Due to their close biochemical properties, purification of individual gingipains is difficult and requires multiple chromatographic steps. In this study, we demonstrate that insertion of a hexahistidine affinity tag upstream of a C-terminal outer membrane translocation signal in RgpB gingipain leads to the secretion of a soluble, mature form of RgpB bearing the affinity tag that can easily be purified by nickel-chelating affinity chromatography. The final product obtained high yielding high purity is biochemically indistinguishable from the native RgpB enzyme.

Porphyromonas gingivalis facilitates the development and progression of destructive arthritis through its unique bacterial peptidylarginine deiminase (PAD).

Rheumatoid arthritis and periodontitis are two prevalent chronic inflammatory diseases in humans and are associated with each other both clinically and epidemiologically. Recent findings suggest a causative link between periodontal infection and rheumatoid arthritis via bacteria-dependent induction of a pathogenic autoimmune response to citrullinated epitopes. Here we showed that infection with viable periodontal pathogen Porphyromonas gingivalis strain W83 exacerbated collagen-induced arthritis (CIA) in a mouse model, as manifested by earlier onset, accelerated progression and enhanced severity of the disease, including significantly increased bone and cartilage destruction. The ability of P. gingivalis to augment CIA was dependent on the expression of a unique P. gingivalis peptidylarginine deiminase (PPAD), which converts arginine residues in proteins to citrulline. Infection with wild type P. gingivalis was responsible for significantly increased levels of autoantibodies to collagen type II and citrullinated epitopes as a PPAD-null mutant did not elicit similar host response. High level of citrullinated proteins was also detected at the site of infection with wild-type P. gingivalis. Together, these results suggest bacterial PAD as the mechanistic link between P. gingivalis periodontal infection and rheumatoid arthritis.

Age-dependent changes in Porphyromonas gingivalis and Prevotella species/phylotypes in healthy gingiva and inflamed/diseased sub-gingival sites.

OBJECTIVES: Early colonisation of oral surfaces by periodontal pathogens presents a significant risk factor for subsequent development of destructive disease affecting tissues that support the dentition. The aims of the present study were to establish the age-dependent relationship between sub-gingival profiles of 22 Prevotella species/phylotypes in children, adolescents and adults from an isolated Aboriginal community and, further, to use this information to identify Prevotella species that could serve as microbial risk indicators. MATERIALS AND METHODS: DNA isolated from sub-gingival plaque samples (three healthy sites and three inflamed/diseased sites) from adults, adolescents and children was screened for Porphyromonas gingivalis load and 22 Prevotella species/phylotypes by species-specific PCR. RESULTS: A noticeable feature in adolescents was the marked increase in colonisation by P. gingivalis across all test sites. The mean number of Prevotella species/phylotypes colonising inflamed/diseased sub-gingival sites increased with age. Progressive partitioning of selected Prevotella species/phylotypes to healthy or inflamed/diseased sites was evident. Prevalence of Prevotella intermedia, Prevotella oral clone P4PB_24 and Prevotella oris increased significantly with age in diseased sites. Similarly, significant age-dependent increase in colonisation of healthy as well as inflamed/diseased sub-gingival sites was apparent for Prevotella oralis, Prevotella multiformis, Prevotella denticola, Prevotella strain P4P_53 and Prevotella oral clone BR014. CONCLUSION: Early colonisation of children by P. gingivalis, P. intermedia and Prevotella oral clone P4PB_24 provides indication of risk for subsequent development of periodontal disease. CLINICAL RELEVANCE: In the present study, the complexity of Prevotella species within gingival sites is explored as a basis for evaluating contribution of Prevotella species to disease.

Inhibition of gingipains by their profragments as the mechanism protecting Porphyromonas gingivalis against premature activation of secreted proteases.

BACKGROUND: Arginine-specific (RgpB and RgpA) and lysine-specific (Kgp) gingipains are secretory cysteine proteinases of Porphyromonas gingivalis that act as important virulence factors for the organism. They are translated as zymogens with both N- and C-terminal extensions, which are proteolytically cleaved during secretion. In this report, we describe and characterize inhibition of the gingipains by their N-terminal prodomains to maintain latency during their export through the cellular compartments. METHODS: Recombinant forms of various prodomains (PD) were analyzed for their interaction with mature gingipains. The kinetics of their inhibition of proteolytic activity along with the formation of stable inhibitory complexes with native gingipains was studied by gel filtration, native PAGE and substrate hydrolysis. RESULTS: PDRgpB and PDRgpA formed tight complexes with arginine-specific gingipains (Ki in the range from 6.2nM to 0.85nM). In contrast, PDKgp showed no inhibitory activity. A conserved Arg-102 residue in PDRgpB and PDRgpA was recognized as the P1 residue. Mutation of Arg-102 to Lys reduced inhibitory potency of PDRgpB by one order of magnitude while its substitutions with Ala, Gln or Gly totally abolished the PD inhibitory activity. Covalent modification of the catalytic cysteine with tosyl-l-Lys-chloromethylketone (TLCK) or H-D-Phe-Arg-chloromethylketone did not affect formation of the stable complex. CONCLUSION: Latency of arginine-specific progingipains is efficiently exerted by N-terminal prodomains thus protecting the periplasm from potentially damaging effect of prematurely activated gingipains. GENERAL SIGNIFICANCE: Blocking progingipain activation may offer an attractive strategy to attenuate P. gingivalis pathogenicity.

Sequence-independent processing site of the C-terminal domain (CTD) influences maturation of the RgpB protease from Porphyromonas gingivalis.

The Gram-negative periodontal pathogen Porphyromonas gingivalis produces a family of outer membrane-anchored proteases, the gingipains, shown to play an essential role in virulence of the organism. The C-terminal domain (CTD) of gingipains and other secreted proteins is known to be the targeting signal for maturation and translocation of the protein through the outer membrane. The CTD is subsequently cleaved during the secretion process. Multiple alignment of various CTDs failed to define a consensus sequence at the putative CTD processing site. Using mutagenesis, we were able to show that cleavage at the site is not dependent on a specific residue and that recognition of the site is independent of local sequence. Interestingly, length of the junction between the CTD and adjacent Ig-like subdomain has a critical influence on post-translational glycan modification of the protein, whereby insertion of additional residues immediately N-terminal to the cleavage site results in failure of glycan modification and release of soluble protease into the culture medium. Various hypotheses are presented to explain these phenomena. Knowledge of the role CTDs play in maturation of gingipains has broader application for understanding maturation of CTD homologues expressed by bacteria of the Bacteriodetes phylum.

pH gradient and distribution of streptococci, lactobacilli, prevotellae, and fusobacteria in carious dentine.

OBJECTIVES: Caries process comprises acidogenic and aciduric bacteria that are responsible for lowering the pH and subsequent destruction of hydroxyapatite matrix in enamel and dentine. The aim of this study was to identify the correlation between the pH gradient of a carious lesion and proportion and distribution of four bacterial genera; lactobacilli, streptococci, prevotellae, and fusobacteria with regard to total load of bacteria. MATERIALS AND METHODS: A total of 25 teeth with extensive dentinal caries were sampled in sequential layers. Using quantitative real-time PCR of 16S rRNA gene, we quantified the total load of bacteria as well as the proportion of the above-mentioned genera following pH measurement of each sample with a fine microelectrode. RESULTS: We demonstrated the presence of a pH gradient across the lesion with a strong association between the quantity of lactobacilli and the lowest pH range (pH 4.5-5.0; p = 0.003). Streptococci had a tendency to occupy the most superficial aspect of the carious lesion but showed no correlation to any pH value. Prevotellae showed clear preference for the pH range 5.5-6.0 (p = 0.042). The total representation of these four genera did not reach more than one quarter of the total bacterial load in most carious samples. CONCLUSION: We revealed differential colonization behavior of bacteria with respect to pH gradient and a lower than expected abundance of lactobacilli and streptococci in established carious lesions. The data indicate the numerical importance of relatively unexplored taxa within the lesion of dentinal caries. CLINICAL RELEVANCE: The gradient nature of pH in the lesion as well as colonization difference of examined bacterial taxa with reference to pH provides a new insight in regard to conservative caries management.

Green synthesis and characterization of α-Mn2O3 nanoparticles for antibacterial activity and efficient visible-light photocatalysis.

In this study, green synthesis, characterizations, photocatalytic performance, and antibacterial applications of α-Mn2O3 nanoparticles are reported. The synthesized nanoparticles were characterized by Fourier transform infrared spectroscopy (FT-IR), powder X-ray diffraction (XRD), transmission electron microscope (TEM), Scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX), Brunauer Emmett Teller (BET), Electrochemical Impedance Spectroscopy (EIS), Photoluminescence (PL), and Differential reflectance spectroscopy (DRS) analysis. The investigation verified that the α-Mn2O3 nanoparticles possessed a cubic structure, with a crystallite size of 23 nm. The SEM and TEM techniques were used to study the nanoscale morphology of α- Mn2O3 nanoparticles, which were found to be spherical with a size of 30 nm. Moreover, the surface area was obtained as 149.9 m2 g-1 utilizing BET analysis, and the band gap was determined to be 1.98 eV by DRS analysis. The photocatalysis performance of the α-Mn2O3 NPs was evaluated for degrading Eriochrome Black T (EBT) dye under visible light and degradation efficiency was 96% in 90 min. The photodegradation mechanism of EBT dye was clarified with the use of radical scavenger agents, and the degradation pathway was confirmed through Liquid Chromatography-Mass Spectrometry (LC-MS) analysis. Additionally, the produced nanoparticles could be extracted from the solution and continued to exhibit photocatalysis even after five repeated runs under the same optimal conditions. Also, the antibacterial activity of green synthesized α-Mn2O3 nanoparticles was investigated by using the broth microdilution method towards Enterococcus faecalis ATCC 29212 (Gram-positive), Staphylococcus aureus ATCC 29213 (Gram-positive), Salmonella typhimurium ATCC 14028 (Gram-negative), Klebsiella pneumoniae ATCC 7881 (Gram-negative), Escherichia coli ATCC 25922 (Gram-negative), Proteus mirabilis ATCC 7002 (Gram-negative), and Pseudomonas aeruginosa ATCC 27853 (Gram-negative) bacterial strains.

Omics analysis unveils changes in the metabolome and lipidome of Caenorhabditis elegans upon polydopamine exposure.

Polydopamine (PDA) is an insoluble biopolymer with a dark brown-black color that forms through the autoxidation of dopamine. Because of its outstanding biocompatibility and durability, PDA holds enormous promise for various applications, both in the biomedical and non-medical domains. To ensure human safety, protect health, and minimize environmental impacts, the assessment of PDA toxicity is important. In this study, metabolomics and lipidomics assessed the impact of acute PDA exposure on Caenorhabditis elegans (C. elegans). The findings revealed a pronounced perturbation in the metabolome and lipidome of C. elegans at the L4 stage following 24 hours of exposure to 100 µg/mL PDA. The changes in lipid composition varied based on lipid classes. Increased lipid classes included lysophosphatidylethanolamine, triacylglycerides, and fatty acids, while decreased species involved in several sub-classes of glycerophospholipids and sphingolipids. Besides, we detected 37 significantly affected metabolites in the positive and 8 in the negative ion modes due to exposure to PDA in C. elegans. The metabolites most impacted by PDA exposure were associated with purine metabolism, biosynthesis of valine, leucine, and isoleucine; aminoacyl-tRNA biosynthesis; and cysteine and methionine metabolism, along with pantothenate and CoA biosynthesis; the citrate cycle (TCA cycle); and beta-alanine metabolism. In conclusion, PDA exposure may intricately influence the metabolome and lipidome of C. elegans. The combined application of metabolomics and lipidomics offers additional insights into the metabolic perturbations involved in PDA-induced biological effects and presents potential biomarkers for the assessment of PDA safety.

Metabolic phenotyping and global functional analysis facilitate metabolic signature discovery for tuberculosis treatment monitoring.

Tracking alterations in polar metabolite and lipid levels during anti-tuberculosis (TB) interventions is an emerging biomarker discovery and validation approach due to its sensitivity in capturing changes and reflecting on the host status. Here, we employed deep plasma metabolic phenotyping to explore the TB patient metabolome during three phases of treatment: at baseline, during intensive phase treatment, and upon treatment completion. Differential metabolites (DMs) in each period were determined, and the pathway-level biological alterations were explored by untargeted metabolomics-guided functional interpretations that bypassed identification. We identified 41 DMs and 39 pathways that changed during intensive phase completion. Notably, levels of certain amino acids including histidine, bile acids, and metabolites of purine metabolism were dramatically increased. The altered pathways included those involved in the metabolism of amino acids, glycerophospholipids, and purine. At the end of treatment, 44 DMs were discovered. The levels of glutamine, bile acids, and lysophosphatidylinositol significantly increased compared to baseline; the levels of carboxylates and hypotaurine declined. In addition, 37 pathways principally associated with the metabolism of amino acids, carbohydrates, and glycan altered at treatment completion. The potential of each DM for diagnosing TB was examined using a cohort consisting of TB patients, those with latent infections, and controls. Logistic regression revealed four biomarkers (taurine, methionine, glutamine, and acetyl-carnitine) that exhibited excellent performance in differential diagnosis. In conclusion, we identified metabolites that could serve as useful metabolic signatures for TB management and elucidated underlying biological processes affected by the crosstalk between host and TB pathogen during treatment.