In-depth Characterization Research Articles

Interplay of luminescence and magnetic phenomena in Mn-doped ZnS zinc blende nanocrystals: Influence of magnetic doping

This research comprehensively investigates the interplay between luminescence and magnetic phenomena in the zinc blende phase of manganese-doped and undoped zinc sulfide. The study involves the synthesis of zinc sulfide nanocrystals through a soft chemical method, followed by an in-depth experimental characterization. Theoretical studies were conducted using a 2 × 2 × 2 supercell model with 64 atoms to explore the impact of native defects and manganese doping on zinc sulfide's the electronic, magnetic, and optical properties. The research findings offer a detailed physical description of magnetic and optic phenomena observed, underpinned by a strong correlation between theoretical predictions and experimental results. An essential contribution of this work is developing a depiction that elucidates the relationship between optical transitions and spin-exchange in the context of these phenomena.

Extensive transmission and variation in a functional receptor for praziquantel resistance in endemic Schistosoma mansoni.

Mass-drug administration (MDA) of human populations using praziquantel monotherapy has become the primary strategy for controlling and potentially eliminating the major neglected tropical disease schistosomiasis. To understand how long-term MDA impacts schistosome populations, we analysed whole-genome sequence data of 570 Schistosoma mansoni samples (and the closely related outgroup species, S. rodhaini) from eight countries incorporating both publicly-available sequence data and new parasite material. This revealed broad-scale genetic structure across countries but with extensive transmission over hundreds of kilometres. We characterised variation across the transient receptor potential melastatin ion channel, TRPMPZQ, a target of praziquantel, which has recently been found to influence praziquantel susceptibility. Functional profiling of TRPMPZQ variants found in endemic populations identified four mutations that reduced channel sensitivity to praziquantel, indicating standing variation for resistance. Analysis of parasite infrapopulations sampled from individuals pre- and post-treatment identified instances of treatment failure, further indicative of potential praziquantel resistance. As schistosomiasis is targeted for elimination as a public health problem by 2030 in all currently endemic countries, and even interruption of transmission in selected African regions, we provide an in-depth genomic characterisation of endemic populations and an approach to identify emerging praziquantel resistance alleles.

From quasi-static to dynamic: Experimental study of mechanical and fracture behaviour of epoxy resin

Epoxy polymers are extensively used in various engineering applications such as aerospace, defence, sports, automotive etc. This article focuses on the in-depth mechanical characterisation of EPOFINE®-1564, a Bisphenol-A-based liquid epoxy resin under various loading conditions. To predict the tensile and compressive behaviour of the representative epoxy resin, quasi-static experiments were performed in the range of 10−4 to 10−2s−1 on Universal testing machine (UTM) while the dynamic experiments were conducted using Split Hopkinson Pressure Bar (SHPB) for high strain rates (1136–2833 s−1). In this study, 3D Digital Image Correlation (DIC) was also used to evaluate the specimen's full-field displacement profile over a wide range of strain rates. Analysis of various mechanical properties such as elastic modulus, yield strength, and ultimate strength, revealed that the epoxy polymer is strain rate dependent within the considered strain rate range. For understanding the fracture behaviour, three-point bend (TPB) experiments were also carried out for both quasi-static (1–10 mm/min) as well as dynamic (10–15 m s-1) regimes. Dynamic fracture experiments were performed using the modified Hopkinson Pressure Bar (MHPB). The fracture toughness was determined through load vs crack mouth opening displacement (CMOD). Fracture toughness was found to increase with the displacement rate due to the significant plastic deformation under quasi-static range. Conversely, it was found to decrease under dynamic loading because of absence of plastic deformation resulting in brittle fracture. The fracture surface of the specimen was examined through a high magnification digital microscope.

P11-04 In-depth xenobiotic metabolism characterization of human in vitro liver models for toxicology

P11-04 In-depth xenobiotic metabolism characterization of human in vitro liver models for toxicology

The FAM13A Long Isoform Regulates Cilia Movement and Coordination in Airway Mucociliary Transport.

Single nucelotide polymorphisms (SNPs) at the FAM13A locus are among the most commonly reported risk alleles associated with chronic obstructive pulmonary disease (COPD) and other respiratory diseases; however, the physiological role of FAM13A is unclear. In humans, two major protein isoforms are expressed at the FAM13A locus: "long" and "short," but their functions remain unknown, partly because of a lack of isoform conservation in mice. We performed in-depth characterization of organotypic primary human airway epithelial cell subsets and show that multiciliated cells predominantly express the FAM13A long isoform containing a putative N-terminal Rho GTPase-activating protein (RhoGAP) domain. Using purified proteins, we directly demonstrate the RhoGAP activity of this domain. In Xenopus laevis, which conserve the long-isoform, Fam13a deficiency impaired cilia-dependent embryo motility. In human primary epithelial cells, long-isoform deficiency did not affect multiciliogenesis but reduced cilia coordination in mucociliary transport assays. This is the first demonstration that FAM13A isoforms are differentially expressed within the airway epithelium, with implications for the assessment and interpretation of SNP effects on FAM13A expression levels. We also show that the long FAM13A isoform coordinates cilia-driven movement, suggesting that FAM13A risk alleles may affect susceptibility to respiratory diseases through deficiencies in mucociliary clearance.

Reduced spinel oxide ZnCo2O4 with tetrahedral Co2+ sites for electrochemical nitrate reduction to ammonia and energy conversion

Electrocatalytic NO3− reduction to ammonia (NRA) at ambient conditions emerges as an appealing solution for green ammonia synthesis. In this work, we prepared a reduced Co-based spinel oxide for efficient ammonia synthesis and energy conversion. The in-depth structural characterization and electrochemical evaluation revealed thatthe introduction of Zn and reduction treatment led to the formation of electron-deficient tetrahedrally coordinated Co2+ sites. The resulting R-ZnCo2O4 exhibited remarkable NH3 production capacity with high NH3 selectivity of 92.2 %, FE of 92.3 %, and yield rate of 5.35 mgNH3 h−1 cm−2 (ca. 26.75 mgNH3 h−1 mgcat−1) under a low potential of − 0.3 V vs. RHE. The NRA pathway on R-ZnCo2O4 was further elucidated through DFT calculations and in situ characterizations. The high NRA efficiency of R-ZnCo2O4 was further explored in a Zn − NO3− battery, which was specified by an open circuit voltage of 1.46 V and a peak-power density of 1.40 mW cm−2, demonstrating its promising application for sustainable energy supply and green ammonia synthesis.

Influence of Thermal Treatment and Granulometry on Physicochemical, Techno-Functional and Nutritional Properties of Lentil Flours.

Legume flours are an increasingly popular food ingredient. Thermal treatments applied prior to milling legumes and granulometry can modify flour properties, altering sensory, digestibility and functional attributes. Raw and treated (soaked and cooked) lentil flours of different granulometry were produced. The applied treatment resulted in an increase in fiber content (25.4 vs. 27.6% for raw and treated lentil flour, respectively) and water absorption capacity. It also led to a decrease in ash content (3.3 vs. 1.8% for raw and treated, respectively) and a darker flour. Treated lentil flour was mainly composed of fractions of high granulometry, which could be beneficial for products where a lower glycemic index is sought, as they demonstrated higher fiber and lower carbohydrate content than the finer fractions. Treated flour may be used as an ingredient in the development of raw products, including beverages and desserts, due to its reduced anti-nutritional compounds' content and enhanced organoleptic aspects. The obtained results allow an in-depth characterization of raw and treated lentils flour with different particle sizes to consider a formal and complete standardization of these flours and for understanding their utility and specific food applications.

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation

The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.

Co-detection of respiratory pathogens among ILI patients: characterization of samples collected during the 2018/19 and 2019/20 pre-pandemic seasons

Influenza-like illness (ILI) patients co-detected with respiratory pathogens exhibit poorer health outcomes than those with single infections. To address the paucity of knowledge concerning the incidence of concurrent respiratory pathogens, their relationships, and the clinical differences between patients detected with single and multiple pathogens, we performed an in-depth characterization of the oropharyngeal samples of primary care patients collected in Genoa (Northwest Italy), during winter seasons 2018/19–2019/20.The apriori algorithm was employed to evaluate the incidence of viral, bacterial, and viral-bacterial pairs during the study period. The grade of correlation between pathogens was investigated using the Phi coefficient. Factors associated with viral, bacterial or viral-bacterial co-detection were assessed using logistic regression.The most frequently identified pathogens included influenza A, rhinovirus, Haemophilus influenzae and Streptococcus pneumoniae. The highest correlations were found between bacterial-bacterial and viral-bacterial pairs, such as Haemophilus influenzae-Streptococcus pneumoniae, adenovirus-Haemophilus influenzae, adenovirus-Streptococcus pneumoniae, RSV-A-Bordetella pertussis, and influenza B Victoria-Bordetella parapertussis. Viruses were detected together at significantly lower rates. Notably, rhinovirus, influenza, and RSV exhibited significant negative correlations with each other. Co-detection was more prevalent in children aged < 4, and cough was shown to be a reliable indicator of viral co-detection.Given the evolving epidemiological landscape following the COVID-19 pandemic, future research utilizing the methodology described here, while considering the circulation of SARS-CoV-2, could further enrich the understanding of concurrent respiratory pathogens.

Linking feed, biodiversity, and filtration performance in a Self-Forming Dynamic Membrane BioReactor (SFD MBR) treating canning wastewater

A bench-scale self-forming dynamic membrane bioreactor (SFD MBR) treating canning wastewater showed instable filtration performance, with a worsening in correspondence of a change in the influent quality. To unveil the possible reasons for such behaviour, a microbial investigation was carried out to complement conventional filterability and settleability tests. The microbial communities of the influent wastewater, the activated sludge, and the filtering sludge cake (dynamic membrane) were characterised through metagenomic and differential abundance analyses. In parallel, the production of exopolymers was measured. The outputs indicate that under the tested conditions the canning wastewater promoted the development of a very peculiar microbial ecosystem, with a strong selection of the genus Thiothrix (relative abundance above 90 %). The Shannon index values in activated sludge were below 2, indicating a very low bacterial diversity. This may have limited the ecosystem resilience towards changes of external conditions, causing instability in the process of the dynamic membrane formation. Furthermore, the diversity analysis showed that the bacterial compositions of the feed and the sludge resulted not significantly linked to each other, confirming the main role of the chemical composition of the influent wastewater on overall process performances. When treating agro-industrial streams, in-depth feed characterisation is recommended in order to prevent the factors that may generate instability in SFD MBR performance.

Hydration structure and dynamics of phosphoric acid and its anions-Ultrafast 2D-IR spectroscopy and abinitio molecular dynamics simulations.

The hydration shells of phosphate ions and phosphate groups of nucleotides and phospholipid membranes display markedly different structures and hydrogen-bond strengths. Understanding phosphate hydration requires insight into the spatial arrangements of water molecules around phosphates and in thermally activated structure fluctuations on ultrafast time scales. Femtosecond two-dimensional infrared spectroscopy of phosphate vibrations, particularly asymmetric stretching vibrations between 1000 and 1200cm-1, and abinitio molecular dynamics (AIMD) simulations are combined to map and characterize dynamic local hydration structures and phosphate-water interactions. Phosphoric acid H3PO4 and its anions H2PO4-, HPO42-, and PO43- are studied in aqueous environments of different pH value. The hydration shells of phosphates providing OH donor groups in hydrogen bonds with the first water layer undergo ultrafast structural fluctuations, which induce a pronounced spectral diffusion of vibrational excitations on a sub-300fs time scale. With a decreasing number of phosphate OH groups, the hydration shell becomes more ordered and rigid. The 2D-IR line shapes observed with hydrated PO43- ions display a pronounced inhomogeneous broadening, reflecting a distribution of hydration geometries without fast equilibration. The AIMD simulations allow for an in-depth characterization of the hydration geometries with different numbers of water molecules in the first hydration layer and different correlation functions of the fluctuating electric field that the water environment exerts on the vibrational phosphate oscillators.

MRNA-1273 vaccination induces polyfunctional memory CD4 and CD8 T cell responses in patients with solid cancers undergoing immunotherapy or/and chemotherapy.

Research has confirmed the safety and comparable seroconversion rates following SARS-CoV-2 vaccination in patients with solid cancers. However, the impact of cancer treatment on vaccine-induced T cell responses remains poorly understood. In this study, we expand on previous findings within the VOICE trial by evaluating the functional and phenotypic composition of mRNA-1273-induced T cell responses in patients with solid tumors undergoing immunotherapy, chemotherapy, or both, compared to individuals without cancer. We conducted an ELISpot analysis on 386 participants to assess spike-specific T cell responses 28 days after full vaccination. Further in-depth characterization of using flow cytometry was performed on a subset of 63 participants to analyze the functional phenotype and differentiation state of spike-specific T cell responses. ELISpot analysis showed robust induction of spike-specific T cell responses across all treatment groups, with response rates ranging from 75% to 80%. Flow cytometry analysis revealed a distinctive cytokine production pattern across cohorts, with CD4 T cells producing IFNγ, TNF, and IL-2, and CD8 T cells producing IFNγ, TNF, and CCL4. Variations were observed in the proportion of monofunctional CD4 T cells producing TNF, particularly higher in individuals without cancer and patients treated with chemotherapy alone, while those treated with immunotherapy or chemoimmunotherapy predominantly produced IFNγ. Despite these differences, polyfunctional spike-specific memory CD4 and CD8 T cell responses were comparable across cohorts. Notably, immunotherapy-treated patients exhibited an expansion of spike-specific CD4 T cells with a terminally differentiated effector memory phenotype. These findings demonstrate that systemic treatment in patients with solid tumors does not compromise the quality of polyfunctional mRNA-1273-induced T cell responses. This underscores the importance of COVID-19 vaccination in patients with solid cancers undergoing systemic treatment.

Single cell, Label free Characterisation of Human Mesenchymal Stromal cell Stemness and Future Growth Potential by Autofluorescence Multispectral Imaging.

To use autofluorescence multispectral imaging (AFMI) to develop a non-invasive assay for the in-depth characterisation of human bone marrow derived mesenchymal stromal cells (hBM-MSCs). hBM-MSCs were imaged by AFMI on gridded dishes, stained for endpoints of interest (STRO-1 positivity, alkaline phosphatase, beta galactosidase, DNA content) then relocated and results correlated. Intensity, texture and morphological features were used to characterise the colour distribution of regions of interest, and canonical discriminant analysis was used to separate groups. Additionally, hBM-MSC lines were cultured to arrest, with AFMI images taken after each passage to investigate whether an assay could be developed for growth potential. STRO-1 positivity could be predicted with a receiver operator characteristic area under the curve (AUC) of 0.67. For spontaneous differentiation this was 0.66, for entry to the cell-cycle it was 0.77 and for senescence it was 0.77. Growth potential (population doublings remaining) was estimated with an RMSPE = 2.296. The Mean Absolute Error of the final prediction model indicated that growth potential could be predicted with an error of ± 1.86 doublings remaining. This non-invasive methodology enabled the in-depth characterisation of hBM-MSCs from a single assay. This approach is advantageous for clinical applications as well as research and stands out for the characterisation of both present status as well as future behaviour. The use of data from five MSC lines with heterogenous AFMI profiles supports potential generalisability.

Genomic insights of Lactiplantibacillus plantarum CNPC024: a potential probiotic strain producing immune-boosting tryptophan-derived metabolites.

Probiogenomics can provide important insights bout probiotic candidate bacteria. This study aimed to perform an in-depth genomic characterization of the probiotic candidate Lactiplantibacillus plantarum CNPC024 to investigate its probiosis mechanisms, identify metabolic pathways that might benefit the host, and improve the safety assessment for this strain to be effectively used as a probiotic. After whole-genome sequencing in Illumina MiSeq platform, the de novo genome assembly resulted in a 3.2Mb draft genome. According to the Average Nucleotide Identity (ANI) analysis with 46 randomly validated probiotic LAB belonging to the Lactobacillaceae family, the strain showed a 99% nucleotide identity with other L. plantarum probiotic species. We identified a set of determinants conferring tolerance to bile salts and low pH conditions, as well as temperature, oxidative and osmotic stressors via the glutathione-glutaredoxin system (Grxs). As a β‑galactosidase‑producing strain, it has the potential to be used in fermented dairy products for lactose-intolerant individuals. There were no significant hits for transferable antibiotic-resistance genes. We also identified gene clusters associated with production of bacteriocins (plantaricins E, F and K). Lastly, we detected metabolic pathways associated with the production of tryptophan-derived metabolites that could potentially modulate the host's immune responses.

Cohort profile: study design and baseline characteristics of an observational longitudinal weight loss cohort and biorepository of patients undergoing sleeve gastrectomy in the USA

PurposeWe developed a comprehensive sleeve gastrectomy (SG) weight loss study cohort and biorepository to uncover mechanisms, biomarkers and predictive factors of weight loss, weight maintenance and amelioration of obesity-related comorbidities....

Physicochemical Characterization of the Oral Biotherapeutic Drug IMUNOR®.

IMUNOR is an oral biotherapeutic drug that had been developed, registered, and approved in 1997 in the Czech Republic and Slovakia. IMUNOR is a dialyzable leukocyte extract (DLE) prepared from swine leukocytes. It is characterized as a mixture of small peptides with molecular weights smaller than 12 kDa and a specific portion of nucleotides. The medical uses of IMUNOR include therapeutic applications within its registered range of indications, primarily for the treatment of immunodeficiencies, allergies, and certain acute or relapsing bacterial infections in adults and children. Despite the long-term clinical application of DLE, with strong evidence of positive therapeutic effects and no serious side effects, a detailed physicochemical specification of this mixture was lacking. We developed several methods for more in-depth physicochemical characterization of IMUNOR, including a spectrophotometric method for quantification of the total protein concentration and total DNA concentration in a mixture, several chromatographic methods for identification of individual components present in significant concentrations in IMUNOR, such as HPLC methods and the Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis method, and characterization of amino acid composition of this mixture. For the investigation of the variability among different batches of IMUNOR, five to nine representative batches from a standard manufacturing process on an industrial scale were utilized. Using the analytical methods, we verified and confirmed the batch-to-batch reproducibility of the biological product IMUNOR.

In-Depth XANES and EXAFS Characterization of the Ag+ Ion Coordination in Dimethyl Sulfoxide Solution.

X-ray absorption near-edge structure (XANES) spectroscopy has been used, in conjunction with extended X-ray absorption fine structure (EXAFS), to determine the coordination structure of the Ag+ ion in a dimethyl sulfoxide (DMSO) solution. From the EXAFS data analysis, the Ag-O first shell distance in DMSO was found to be 2.31(3) Å, with 4.1(5) oxygen atoms surrounding the Ag+ ion, in fair agreement with previous results. This technique did not allow us to determine the geometry of the 4-fold coordination complex and a quantitative analysis of the XANES region was carried out to shed light on this issue. The XANES data analysis confirmed the presence of a four-coordinated complex, unambiguously showing that a regular tetrahedral [Ag(DMSO)4]+ complex is formed when silver triflate is dissolved in DMSO solution.

Nanostructure silver absorbance with polarized light spectroscopy (PLS) and mobile imaging

This study presents a novel interdisciplinary approach for characterizing the optical properties of nanostructured silver films, combining methodologies from polarized light spectroscopy (PLS) and mobile app-based spectroscopic image detection. Silver nanofilms were deposited using electron beam evaporation (EBE) and subsequently analyzed for their absorbance across the visible light spectrum through PLS spectroscopy. The innovative aspect of this study lies in the validation of PLS spectral data using a mobile application developed with MIT App Inventor, which analyzes the intensity of light beams captured in images taken by a smartphone. The findings indicate that the silver nanofilm exhibits peak absorbance at approximately 400 nm within the violet region, corroborated by the mobile app’s data, which shows the lowest light intensity. However, discrepancies were observed from 500 to 600 nm, likely due to ambient light interferences and inherent optical phenomena such as diffraction, reflection, and refraction. Despite these deviations, the app’s readings closely align with the PLS data, supporting the film’s selective absorption properties. This study demonstrates the potential of this multidisciplinary technique in nanomaterial research, highlighting the application of nanotechnology in material science and the transformative potential of integrating software engineering for in-depth material characterization. These findings open avenues for advancements in both academic and practical applications.

Exploring the manganese-dependent interaction between a transcription factor and its corresponding DNA: insights from gas-phase electrophoresis on a nES GEMMA instrument

Manganese ion homeostasis is vital for bacteria and is achieved via manganese-dependent transcription factors. Manganese mediation of transcription factor attachment to the corresponding oligonucleotide sequences can be investigated, e.g. via electrophoretic mobility shift assays (EMSA). Formation of specific biocomplexes leads to differences in the migration pattern upon gel electrophoresis. Focusing on electrophoresis in the gas-phase, applying a nano electrospray gas-phase electrophoretic mobility molecular analyzer (nES GEMMA) also known as nES differential mobility analyzer (nES DMA), and on transcription factors (MntR proteins) from Bacillus subtilis and Mycobacterium tuberculosis, we took interest in the gas-phase electrophoresis of the corresponding biospecific complexes. We compared nES GEMMA, separating analytes in the nanometer regime (a few to several hundred nm in diameter) in the gas-phase in their native state according to particle size, to EMSA data. Indeed we were able to demonstrate manganese-mediated attachment of MntR to target genomic sequences with both analytical techniques. Despite some inherent pitfalls of the nES GEMMA method like analyte/instrument surface interactions, we were able to detect the target complexes. Moreover, we were able to calculate the molecular weight (MW) of the obtained species by application of a correlation function based on nES GEMMA obtained data. As gas-phase electrophoresis also offers the possibility of offline hyphenation to orthogonal analysis techniques, we are confident that nES GEMMA measurements are not just complementary to EMSA, but will offer the possibility of further in-depth characterization of biocomplexes in the future.Graphical

Abstract 30: In-Depth Characterization of B-Lineage Populations Arising During Cord Blood CD34+ HSPC Differentiation for ETV6::RUNX1 Progenitor Identification

Abstract 30: In-Depth Characterization of B-Lineage Populations Arising During Cord Blood CD34+ HSPC Differentiation for ETV6::RUNX1 Progenitor Identification