Tissue adaptation and clonal segregation of human memory T cells in barrier sites.

T lymphocytes migrate to barrier sites after exposure to pathogens, providing localized immunity and long-term protection. Here, we obtained blood and tissues from human organ donors to examine T cells across major barrier sites (skin, lung, jejunum), associated lymph nodes, lymphoid organs (spleen, bone marrow), and in circulation. By integrating single-cell protein and transcriptome profiling, we demonstrate that human barrier sites contain tissue-resident memory T (TRM) cells that exhibit site-adapted profiles for residency, homing and function distinct from circulating memory T cells. Incorporating T cell receptor and transcriptome analysis, we show that circulating memory T cells are highly expanded, display extensive overlap between sites and exhibit effector and cytolytic functional profiles, while TRM clones exhibit site-specific expansions and distinct functional capacities. Together, our findings indicate that circulating T cells are more disseminated and differentiated, while TRM cells exhibit tissue-specific adaptation and clonal segregation, suggesting that strategies to promote barrier immunity require tissue targeting.

Tissue Determinants of Human NK Cell Development, Function, and Residence.

Immune responses in diverse tissue sites are critical for protective immunity and homeostasis. Here, we investigate how tissue localization regulates the development and function of human natural killer (NK) cells, innate lymphocytes important for anti-viral and tumor immunity. Integrating high-dimensional analysis of NK cells from blood, lymphoid organs, and mucosal tissue sites from 60 individuals, we identify tissue-specific patterns of NK cell subset distribution, maturation, and function maintained across age and between individuals. Mature and terminally differentiated NK cells with enhanced effector function predominate in blood, bone marrow, spleen, and lungs and exhibit shared transcriptional programs across sites. By contrast, precursor and immature NK cells with reduced effector capacity populate lymph nodes and intestines and exhibit tissue-resident signatures and site-specific adaptations. Together, our results reveal anatomic control of NK cell development and maintenance as tissue-resident populations, whereas mature, terminally differentiated subsets mediate immunosurveillance through diverse peripheral sites. VIDEO ABSTRACT.

Distinct antibody responses to SARS-CoV-2 in children and adults across the COVID-19 clinical spectrum.

Clinical manifestations of COVID-19 caused by the new coronavirus SARS-CoV-2 are associated with age1,2. Adults develop respiratory symptoms, which can progress to acute respiratory distress syndrome (ARDS) in the most severe form, while children are largely spared from respiratory illness but can develop a life-threatening multisystem inflammatory syndrome (MIS-C)3-5. Here, we show distinct antibody responses in children and adults after SARS-CoV-2 infection. Adult COVID-19 cohorts had anti-spike (S) IgG, IgM and IgA antibodies, as well as anti-nucleocapsid (N) IgG antibody, while children with and without MIS-C had reduced breadth of anti-SARS-CoV-2-specific antibodies, predominantly generating IgG antibodies specific for the S protein but not the N protein. Moreover, children with and without MIS-C had reduced neutralizing activity as compared to both adult COVID-19 cohorts, indicating a reduced protective serological response. These results suggest a distinct infection course and immune response in children independent of whether they develop MIS-C, with implications for developing age-targeted strategies for testing and protecting the population.

Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood.

Infancy and childhood are critical life stages for generating immune memory to protect against pathogens; however, the timing, location, and pathways for memory development in humans remain elusive. Here, we investigated T cells in mucosal sites, lymphoid tissues, and blood from 96 pediatric donors aged 0-10 years using phenotypic, functional, and transcriptomic profiling. Our results revealed that memory T cells preferentially localized in the intestines and lungs during infancy and accumulated more rapidly in mucosal sites compared with blood and lymphoid organs, consistent with site-specific antigen exposure. Early life mucosal memory T cells exhibit distinct functional capacities and stem-like transcriptional profiles. In later childhood, they progressively adopt proinflammatory functions and tissue-resident signatures, coincident with increased T cell receptor (TCR) clonal expansion in mucosal and lymphoid sites. Together, our findings identify staged development of memory T cells targeted to tissues during the formative years, informing how we might promote and monitor immunity in children.

Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19.

Immune response dynamics in coronavirus disease 2019 (COVID-19) and their severe manifestations have largely been studied in circulation. Here, we examined the relationship between immune processes in the respiratory tract and circulation through longitudinal phenotypic, transcriptomic, and cytokine profiling of paired airway and blood samples from patients with severe COVID-19 relative to heathy controls. In COVID-19 airways, T cells exhibited activated, tissue-resident, and protective profiles; higher T cell frequencies correlated with survival and younger age. Myeloid cells in COVID-19 airways featured hyperinflammatory signatures, and higher frequencies of these cells correlated with mortality and older age. In COVID-19 blood, aberrant CD163+ monocytes predominated over conventional monocytes, and were found in corresponding airway samples and in damaged alveoli. High levels of myeloid chemoattractants in airways suggest recruitment of these cells through a CCL2-CCR2 chemokine axis. Our findings provide insights into immune processes driving COVID-19 lung pathology with therapeutic implications for targeting inflammation in the respiratory tract.

Axes of heterogeneity in human tissue-resident memory T cells.

Tissue-resident memory T cells (TRM) represent a dedicated layer of localized immune memory in virtually every organ throughout the human body. By virtue of their long-term residence in disparate tissues, TRM are shaped by a myriad of site-specific influences and exhibit remarkable heterogeneity in form and function. Here, we review the major axes by which TRM vary, including their surface phenotypes, transcriptional programming, and the tissue-specific adaptations that accrue over their tenancy. We discuss how localization within distinct anatomic niches both within and across major organ systems shapes TRM identity and examine mechanisms and prevailing models for TRM generation. Understanding the drivers of differentiation, function and maintenance of the various subpopulations that together define the TRM lineage may hold the key to unlocking the full potential of TRM to promote localized and protective tissue immunity throughout the body.

Theoretical dynamics studies of the CH3 + HBr → CH4 + Br reaction: effects of isotope substitution and vibrational excitation of CH3.

The rate coefficient for two deuterium substituted isotopologues of reaction CH3 + HBr → CH4 + Br has been determined using the quasiclassical trajectory (QCT) method. We used the analytical potential energy surface (PES) fitted to high-level ab initio points in earlier work. The PES exhibits a pre-reaction van der Waals complex and a submerged potential barrier. The rate coefficients of the deuterated isotopologue reactions, similarly to the pure-protium isotopologue, show significant deviation from the Arrhenius law, namely, the activation energy is negative below about 600 K and positive above it: k[CH3 + DBr] = 1.35 × 10-11 exp(- 2472/T) + 5.85 × 10-13 exp(335/T) and k[CD3 + HBr] = 2.73 × 10-11 exp(- 2739/T) + 1.46 × 10-12 exp(363/T). The CH3 + DBr reaction is slower by a factor of 1.8, whereas CD3 + HBr isotopologue is faster by a factor of 1.4 compared to the HBr + CH3 system across a wide temperature range. The isotope effects are interpreted in terms of the properties of various regions of the PES. Quantum state-resolved simulations revealed that the reaction of CH3 with HBr becomes slower when any of the vibrational modes of the methyl radical is excited. This contradicts the assumption that vibrational excitation of methyl radicals enhances its reactivity, which is of historical importance: this assumption was used as an argument against the existence of negative activation energy in a decade-long controversy in the 1980s and 1990s.

Characters evolution of Encyclia (Laeliinae-Orchidaceae) reveals a complex pattern not phylogenetically determined: insights from macro- and micromorphology.

Encyclia is the second-largest genus in the neotropical subtribe Laeliinae (Orchidaceae) and has more than 150 species, which are characterized by fairly consistent flower morphology. Its taxonomy and species boundaries, however, seem to be still under debate. In the present study, we first examined the lip micromorphology of 61 species of Encyclia sensu stricto. We correlated our results with external flower morphology and phylogenetic analyses performed on a combined dataset that included both nuclear (ITS, Xdh, PhyC) and plastid markers (ycf1, rpl32, and trnL-trnF). Phylogenetic reconstruction showed that Encyclia sensu stricto species form a coherent, monophyletic group. However, it is difficult to determine the relationships between the different groups within one larger clade. The groups all form distinct lineages that evolved from a common ancestor. The UPGMA cluster analysis for the seven qualitative micromorphological features clearly divides the genus into two main groups, the larger of which is further subdivided into two subgroups. None of these, however, overlap with any of the phylogeographic units distinguished in previously published papers or in presented article. It is worth noting that the groups resulting from the UPGMA analysis cannot be defined by macromorphological features. The pattern of similarities between species, taking into account both macro- and micromorphological features, is eminently mosaic in nature, and only a multifaceted approach can explain this enigmatic group.

Experimental and Theoretical Study of the Kinetics of the CH3 + HBr → CH4 + Br Reaction and the Temperature Dependence of the Activation Energy of CH4 + Br → CH3 + HBr.

The rate coefficient of the reaction of CH3 with HBr was measured and calculated in the temperature range 225-960 K. The results of the measurements performed in a flow apparatus with mass spectrometric detection agree very well with the quasiclassical trajectory calculations performed on a previously developed potential energy surface. The experimental rate coefficients are described well with a double-exponential fit, k1(exp) = [1.44 × 10-12 exp(219/T) + 6.18 × 10-11 exp(-3730/T)] cm3 molecule-1 s-1. The individual rate coefficients below 500 K accord with the available experimental data as does the slightly negative activation energy in this temperature range, -1.82 kJ/mol. At higher temperatures, the activation energy was found to switch sign and it rises up to about an order of magnitude larger positive value than that below 500 K, and the rate coefficient is about 50% larger at 960 K than that around room temperature. The rate coefficients calculated with the quasiclassical trajectory method display the same tendencies and are within about 8% of the experimental data between 960 and 300 K and within 25% below that temperature. The significant variation of the magnitude of the activation energy can be reconciled with the tabulated heats of formation only if the activation energy of the reverse CH4 + Br reaction also significantly increases with the temperature.

Polyatomic radiative association by quasiclassical trajectory calculations: Formation of HCN and HNC molecules in H + CN collisions.

We have developed the polyatomic extension of the established [M. Gustafsson, J. Chem. Phys. 138, 074308 (2013)] classical theory of radiative association in the absence of electronic transitions. The cross section and the emission spectrum of the process is calculated by a quasiclassical trajectory method combined with the classical Larmor formula which can provide the radiated power in collisions. We have also proposed a Monte Carlo scheme for efficient computation of ro-vibrationally quantum state resolved cross sections for radiative association. Besides the method development, the global potential energy and dipole surfaces for H + CN collisions have been calculated and fitted to test our polyatomic semiclassical method.

Comparative Evaluation of the Repair Bond Strength of Dental Resin Composite after Sodium Bicarbonate or Aluminum Oxide Air-Abrasion.

The dental prophylactic cleaning of a damaged resin-based composite (RBC) restoration with sodium bicarbonate can change the surface characteristics and influence the repair bond strength. The purpose of this study was to compare the effect of sodium bicarbonate (SB) and aluminum oxide (AO) surface treatments on the microtensile bond strength (µTBS) of repaired, aged RBC. Bar specimens were prepared from microhybrid RBC and aged in deionized water for 8 weeks. Different surface treatments (AO air-abrasion; SB air-polishing), as well as cleaning (phosphoric acid, PA; ethylene-diamine-tetraacetic-acid, EDTA) and adhesive applications (single bottle etch-and-rinse, ER; universal adhesive, UA), were used prior to the application of the repair RBC. Not aged and aged but not surface treated RBCs were used as positive and negative controls, respectively. The repaired blocks were cut into sticks using a precision grinding machine. The specimens were tested for tensile fracture and the µTBS values were calculated. Surface characteristics were assessed using scanning electron microscopy. AO-PA-UA (62.6 MPa) showed a 20% increase in µTBS compared to the NC (50.2 MPa), which proved to be the most significant. This was followed by SB-EDTA-UA (58.9 MPa) with an increase of 15%. In addition to AO-PA-UA, SB-EDTA-UA could also be a viable alternative in the RBC repair protocol.

Serum Total Antioxidant Capacity (TAC) and TAC/Lymphocyte Ratio as Promising Predictive Markers in COVID-19.

SARS-CoV-2 infection might cause a critical disease, and patients' follow-up is based on multiple parameters. Oxidative stress is one of the key factors in the pathogenesis of COVID-19 suggesting that its level could be a prognostic marker. Therefore, we elucidated the predictive value of the serum non-enzymatic total antioxidant capacity (TAC) and that of the newly introduced TAC/lymphocyte ratio in COVID-19. We included 61 COVID-19 (n = 27 ward, n = 34 intensive care unit, ICU) patients and 29 controls in our study. Serum TAC on admission was measured by an enhanced chemiluminescence (ECL) microplate assay previously validated by our research group. TAC levels were higher (p < 0.01) in ICU (median: 407.88 µmol/L) than in ward patients (315.44 µmol/L) and controls (296.60 µmol/L). Besides the classical parameters, both the TAC/lymphocyte ratio and TAC had significant predictive values regarding the severity (AUC-ROC for the TAC/lymphocyte ratio: 0.811; for TAC: 0.728) and acute kidney injury (AUC-ROC for the TAC/lymphocyte ratio: 0.747; for TAC: 0.733) in COVID-19. Moreover, the TAC/lymphocyte ratio had significant predictive value regarding mortality (AUC-ROC: 0.752). Serum TAC and the TAC/lymphocyte ratio might offer valuable information regarding the severity of COVID-19. TAC measured by our ECL microplate assay serves as a promising marker for the prediction of systemic inflammatory diseases.

Microbiological Studies on the Influence of Essential Oils from Several Origanum Species on Respiratory Pathogens.

Essential oils (EOs) with established and well-known activities against human pathogens might become new therapeutics in multidrug-resistant bacterial infections, including respiratory tract infections. The aim of this study was to evaluate the antimicrobial activity of EOs obtained from several samples of Origanum vulgare, O. syriacum, and O. majorana cultivated in Poland. EOs were analyzed by GC-MS and tested against four bacterial strains: Staphylococcus aureus (MRSA), Haemophilus influenzae, Haemophilus parainfluenzae, and Pseudomonas aeruginosa. Chemical analyses showed that the Eos were characterized by a high diversity in composition. Based on the chemical data, four chemotypes of Origanum EOs were confirmed. These were carvacrol, terpineol/sabinene hydrate, caryophyllene oxide, and thymol chemotypes. Thin-layer chromatography-bioautography confirmed the presence of biologically active antibacterial components in all tested EOs. The highest number of active spots were found among EOs with cis-sabinene hydrate as the major compound. On the other hand, the largest spots of inhibition were characteristic to EOs of the carvacrol chemotype. Minimal inhibitory concentrations (MICs) were evaluated for the most active EOs: O. vulgare 'Hirtum', O. vulgare 'Margarita', O. vulgare 'Hot & Spicy', O. majorana, and O. syriacum (I) and (II); it was shown that both Haemophilus strains were the most sensitive with an MIC value of 0.15 mg/mL for all EOs. O. majorana EO was also the most active in the MIC assay and had the highest inhibitory rate in the anti-biofilm assay against all strains. The most characteristic components present in this EO were the trans-sabinene hydrate and terpinen-4-ol. The strain with the least sensitivity was the MRSA with an MIC of 0.6 mg/mL for all EOs except for O. majorana, where the MIC value reached 0.3 mg/mL. Scanning electron microscopy performed on the Haemophilus influenzae and Haemophilus parainfluenzae biofilms showed a visible decrease in the appearance of bacterial clusters under the influence of O. majorana EO.

Four-Dimensional Scaling of Dipole Polarizability in Quantum Systems.

Polarizability is a key response property of physical and chemical systems, which has an impact on intermolecular interactions, spectroscopic observables, and vacuum polarization. The calculation of polarizability for quantum systems involves an infinite sum over all excited (bound and continuum) states, concealing the physical interpretation of polarization mechanisms and complicating the derivation of efficient response models. Approximate expressions for the dipole polarizability, α, rely on different scaling laws α∝R^{3}, R^{4}, or R^{7}, for various definitions of the system radius R. Here, we consider a range of single-particle quantum systems of varying spatial dimensionality and having qualitatively different spectra, demonstrating that their polarizability follows a universal four-dimensional scaling law α=C(4µq^{2}/ℏ^{2})L^{4}, where µ and q are the (effective) particle mass and charge, C is a dimensionless excitation-energy ratio, and the characteristic length L is defined via the L^{2} norm of the position operator. This unified formula is also applicable to many-particle systems, as shown by accurately predicting the dipole polarizability of 36 atoms, 1641 small organic molecules, and Bloch electrons in periodic systems.

Theoretical dynamics studies of the CH3 + HBr → CH4 + Br reaction: integral cross sections, rate constants and microscopic mechanism.

Quantum and quasi-classical dynamics calculations have been performed for the reaction of HBr with CH3. The accurate ab initio-based potential energy surface function developed earlier for this reaction displays a potential well corresponding to a reactant complex and a submerged potential barrier. The integral cross sections were calculated on this potential energy surface using both a six-degree-of-freedom reduced dimensional quantum dynamics and the quasi-classical trajectory method and very good agreement was found between the two approaches. The cross sections were found to diverge when the collision energy decreases, indicating that the reactant attraction is responsible for the dynamics at low collision energy. The quantum mechanical and the quasi-classical rate constants also agree very well and almost exactly reproduce the experimental results at low temperatures up to 540 K. The negative activation energy observed experimentally is confirmed by the calculations and is a consequence of the long-range attraction between the reactants. From the classical trajectories mechanistic details have been extracted. It is found that at very low collision energy, the reacting system crosses the potential barrier because the forces within the complex guide them, although some 30% is reflected from the product side of the barrier. When the collision energy increases, the system does not follow the most favorable path and the reactants are, with increasing probability, reflected from the repulsive walls of the nonreactive parts of the reactants, providing a picture beyond the decreasing excitation function.

Anodic Polymerization of Phenylphenols in Methyl Isobutyl Ketone and Mesityl Oxide: Incorporation of a Cavitand into the Layers Formed for Sensing Phenols in Organic Media.

The electropolymerization of three phenylphenol isomers was studied in methyl isobutyl ketone and mesityl oxide, and the remarkable differences highlighted the importance of the carbon-carbon double bond in mesityl oxide. In the case of each substrate, a brownish deposit formed during the electrooxidation. The obvious difference between the polymers formed from the two solvents was recognized via voltammetric signal enhancement of 4-methoxyphenol and 4-chlorophenol, and it was only observed in the case of mesityl oxide. The experiments highlighted that incorporation of a cavitand with biphenyl groups on the upper rim of the polymers of phenylphenols improved the results to a small extent. The cavitand was, itself, electroactive without any fouling effect. As 2-phenylphenol is by far the cheapest of the three isomers, a cavitand was incorporated into its polymer, which was exploited to solve analytical problems while mesityl oxide was used as solvent. Useful quantifications were achieved in organic solvents; however, it failed under aqueous conditions due to the high hydrophobicity of the deposit. Application of differential pulse voltammetry for 4-methoxyphenol and 4-chlorophenol gave detection limits of 9.28 and 50.8 µM in acetonitrile, respectively. This procedure resulted in the immobilization of cavitand derivatives onto the electrode's surface, and the layer formed offered selective sensing of phenols by electrochemical methods.

Immortelle (Helichrysum italicum (Roth) G. Don) Essential Oil Showed Antibacterial and Biofilm Inhibitory Activity against Respiratory Tract Pathogens.

The biofilm formation of bacteria in different parts of the human body can influence the success of antibiotic therapy. Essential oils (EOs) and their components are becoming increasingly popular in point of view of medicinal applications, because of their antibacterial efficacy. The immortelle EO has been used traditionally as an expectorant; however, there are no studies summarizing its antibacterial effect against respiratory tract bacteria. Our aim was to investigate the antibacterial and biofilm inhibitory activity of immortelle (Helichrysum italicum) EO against respiratory tract pathogens such as Haemophilus influenzae, H. parainfluenzae, Pseudomonas aeruginosa and Streptococcus pneumoniae. In order to prove the antibacterial effect of the immortelle EO, broth microdilution and biofilm inhibition tests, and membrane damage assay were investigated. Scanning electron microscopy was used to identify the structural modifications in bacterial cells. Our results showed that immortelle EO has antibacterial and anti-biofilm effects against respiratory tract bacteria used in this study. H. parainfluenzae was the most sensitive to each treatment, however, P. aeruginosa was the most resistant bacteria. In conclusion, the studied EO may have a role in the treatment of respiratory tract infections due to their antibacterial and anti-biofilm activity.

Biomonitoring and assessment of toxic element contamination in floodplain sediments and soils using fluorescein diacetate (FDA) enzymatic activity measurements: evaluation of possibilities and limitations through the case study of the Drava River floodplain.

The EU Water Framework Directive requires the monitoring and evaluation of surface water sediment quality based on the assessment of risk posed by contamination on the biotic receptors. Floodplain sediments are important receptors of potentially toxic element (PTE) contamination from the upstream catchment areas, and floodplains host climate-sensitive riverine ecosystems and fertile agricultural areas at the same time. This study investigates the effect of PTE contamination on microbial communities in floodplain sediments and soils using the fast, inexpensive and reliable fluorescein diacetate (FDA) method in order to estimate its applicability for sediment quality monitoring and preliminary toxicity-based risk assessment. Sediment and soil samples were collected from the actively flooded alluvial plain and the river terrace areas along a 130-km stretch of the large Drava River floodplain known to be widely contaminated by historical mining, smelting and the associated industry in the upstream Alpine region. Results of detailed data analysis show that the total microbial activity represented by the measured FDA values is related to PTE (As, Cu, Zn, Cd, Pb) concentrations, but this relationship shows significant heterogeneity and depends on the spatial location and on the soil properties such as organic matter content, dissolved salt and nutrient content, and it is specific to the toxic elements. Results show that some microbe species appear to be able to adapt to the elevated PTE concentrations in toxic soil micro-environments, over time. Despite the observed heterogeneity of microbial activity, the results revealed a breakpoint in the FDA dataset around the FDA = 3 FC (fluorescein concentration) value suggesting that microbial activity is controlled by thresholds.

Phenotypes to remember: Evolutionary developmental memory capacity and robustness.

There is increased awareness of the possibility of developmental memories resulting from evolutionary learning. Genetic regulatory and neural networks can be modelled by analogous formalism raising the important question of productive analogies in principles, processes and performance. We investigate the formation and persistence of various developmental memories of past phenotypes asking how the number of remembered past phenotypes scales with network size, to what extent memories stored form by Hebbian-like rules, and how robust these developmental "devo-engrams" are against networks perturbations (graceful degradation). The analogy between neural and genetic regulatory networks is not superficial in that it allows knowledge transfer between fields that used to be developed separately from each other. Known examples of spectacular phenotypic radiations could partly be accounted for in such terms.

The Role of Zero-Point Vibration and Reactant Attraction in Exothermic Bimolecular Reactions with Submerged Potential Barriers: Theoretical Studies of the R + HBr → RH + Br (R = CH3, HO) Systems.

The dynamics of the reactions CH3 + HBr → CH4 + Br and HO + HBr → H2O + Br have been studied using the quasiclassical trajectory method to explore the interplay of the vibrational excitation of the breaking bond and the potential energy surface characterized by a prereaction van der Waals well and a submerged barrier to reaction. The attraction between the reactants is favorable for the reaction, because it brings together the reactants without any energy investment. The reaction can be thought to be controlled by capture. The trajectory calculations indeed provide excitation functions typical to capture: the reaction cross sections diverge when the collision energy is reduced toward zero. Excitation of reactant vibration accelerates both reactions. The barrier on the potential surface is so early that the coupling between the degrees of freedom at the saddle point geometry is negligible. However, the trajectory calculations show that when the breaking bond is stretched at the time of the encounter, an attractive force arises, as if the radical approached a HBr molecule whose bond is partially broken. As a result, the dynamics of the reaction are controlled more by the temporary "dynamical", vibrationally induced than by the "static" van der Waals attraction even when the reactants are in vibrational ground state. The cross sections are shown to drop to very small values when the amplitude of the breaking bond's vibration is artificially reduced, which provides an estimate of the reactivity due to the "static" attraction. Without zero-point vibration these reactions would be very slow, which is a manifestation of a unique quantum effect. Reactions where the reactivity is determined by dynamical factors such as the vibrationally enhanced attraction are found to be beyond the range of applicability of Polanyi's rules.