New Processes for Ionizing Nonvolatile Compounds in Mass Spectrometry: The Road of Discovery to Current State-of-the-Art.

This Perspective covers discovery and mechanistic aspects as well as initial applications of novel ionization processes for use in mass spectrometry that guided us in a series of subsequent discoveries, instrument developments, and commercialization. Vacuum matrix-assisted ionization on an intermediate pressure matrix-assisted laser desorption/ionization source without the use of a laser, high voltages, or any other added energy was simply unbelievable, at first. Individually and as a whole, the various discoveries and inventions started to paint, inter alia, an exciting new picture and outlook in mass spectrometry from which key developments grew that were at the time unimaginable, and continue to surprise us in its simplistic preeminence. We, and others, have demonstrated exceptional analytical utility. Our current research is focused on how best to understand, improve, and use these novel ionization processes through dedicated platforms and source developments. These ionization processes convert volatile and nonvolatile compounds from solid or liquid matrixes into gas-phase ions for analysis by mass spectrometry using, e.g., mass-selected fragmentation and ion mobility spectrometry to provide accurate, and sometimes improved, mass and drift time resolution. The combination of research and discoveries demonstrated multiple advantages of the new ionization processes and established the basis of the successes that lead to the Biemann Medal and this Perspective. How the new ionization processes relate to traditional ionization is also presented, as well as how these technologies can be utilized in tandem through instrument modification and implementation to increase coverage of complex materials through complementary strengths.

Contributions and future potential of animal models for geroscience research on sensory systems.

Sensory systems mediate our social interactions, food intake, livelihoods, and other essential daily functions. Age-related decline and disease in sensory systems pose a significant challenge to healthy aging. Research on sensory decline in humans is informative but can often be difficult, subject to sampling bias, and influenced by environmental variation. Study of animal models, including mice, rats, rabbits, pigs, cats, dogs, and non-human primates, plays a complementary role in biomedical research, offering advantages such as controlled conditions and shorter lifespans for longitudinal study. Various species offer different advantages and limitations but have provided key insights in geroscience research. Here we review research on age-related decline and disease in vision, hearing, olfaction, taste, and touch. For each sense, we provide an epidemiological overview of impairment in humans, describing the physiological processes and diseases for each sense. We then discuss contributions made by research on animal models and ideas for future research. We additionally highlight the need for integrative, multimodal research across the senses as well as across disciplines. Long-term studies spanning multiple generations, including on species with longer life spans, are also highly valuable. Overall, integrative studies of appropriate animal models have high translational potential for clinical applications, the development of novel diagnostics, therapies, and medical interventions and future research will continue to close gaps in these areas. Research on animal models to improve understanding of the biology of the aging senses and improve the healthspan and additional research on sensory systems hold special promise for new breakthroughs.

Lamina Cribrosa Microstructure in Nonhuman Primates With Naturally Occurring Peripapillary Retinal Nerve Fiber Layer Thinning.

Purpose: The lamina cribrosa (LC) is hypothesized to be the site of initial axonal damage in glaucoma with the circumpapillary retinal nerve fiber layer thickness (RNFL-T) widely used as a standard metric for quantifying the glaucomatous damage. The purpose of this study was to determine in vivo, 3-dimensional (3D) differences in the microstructure of the LC in eyes of nonhuman primates (NHPs) with naturally occurring glaucoma. Methods: Spectral-domain optical coherence tomography (OCT) scans (Leica, Chicago, IL, USA) of the optic nerve head were acquired from a colony of 50 adult rhesus monkeys suspected of having high prevalence of glaucoma. The RNFL-T was analyzed globally and in quadrants using a semi-automated segmentation software. From a set of 100 eyes, 18 eyes with the thinnest global RNFL-T were selected as the study group and 18 eyes with RNFL-T values around the 50th percentile were used as controls. A previously described automated segmentation algorithm was used for LC microstructure analysis. Parameters included beam thickness, pore diameter and their ratio (beam-to-pore ratio [BPR]), pore area and shape parameters, beam and pore volume, and connective tissue volume fraction (CTVF; beam volume/total volume). The LC microstructure was analyzed globally and in the following volumetric sectors: quadrants, central and peripheral lamina, and three depth slabs (anterior, middle, and posterior). Results: Although no significant difference was detected between groups for age, weight, or disc size, the study group had significantly thinner RNFL than the control group (P < 0.01). The study group had significantly smaller global and sectoral pore diameter and larger BPR compared with the control group. Across eyes, the global RNFL-T was associated positively with pore diameter globally. BPR and CTVF were significantly and negatively associated with the corresponding RNFL-T in the superior quadrant. Conclusions: Global and sectoral microstructural differences were detected when comparing thin and normal RNFL-T eyes. Whether these LC differences are the cause of RNFL damage or the result of remodeling of the LC requires further investigation. Translational Relevance: Our findings indicate structural alterations in the LC of NHP exhibiting natural thinning of the RNFL, a common characteristic of glaucomatous damage.

A first-in-kind MAPK13 inhibitor that can correct stem cell reprogramming and post-injury disease.

The stress kinase MAPK13 (aka p38δ-MAPK) is an attractive entry point for therapeutic intervention because it regulates the structural remodeling that can develop after epithelial barrier injury in the lung and likely other tissue sites. However, a selective, safe, and effective MAPK13 inhibitor is not yet available for experimental or clinical application. Here we identify a first-in-kind MAPK13 inhibitor using structure-based drug design combined with a screening funnel for cell safety and molecular specificity. This inhibitor (designated NuP-4) down-regulates basal-epithelial stem cell reprogramming, structural remodeling, and pathophysiology equivalently to Mapk13 gene-knockout in mouse and mouse organoid models of post-viral lung disease. This therapeutic benefit persists after stopping treatment as a sign of disease modification and attenuates key aspects of inflammation and remodeling as an indication of disease reversal. Similarly, NuP-4 treatment can directly control cytokine-stimulated growth, immune activation, and mucinous differentiation in human basal-cell organoids. The data thereby provide a new tool and potential fix for long-term stem cell reprogramming after viral injury and related conditions that require MAPK13 induction-activation.

The relationship of speech perception and speech production: It's complicated.

A widely held belief is that speech perception and speech production are tightly linked, with each modality available to help with learning in the other modality. This positive relationship is often summarized as perception and production being "two sides of the same coin." There are, indeed, many situations that have shown this mutually supportive relationship. However, there is a growing body of research showing very different results, with the modalities operating independently, or even in opposition to each other. We review the now-sizeable literature demonstrating the negative effect that speech production can have on perceptual learning of speech, at multiple levels (particularly at the lexical and sublexical levels). By comparing the situations that show this pattern with ones in which more positive interactions occur, we provide an initial account of why the different outcomes are found, identifying factors that lead to either positive or negative effects of production on perception. The review clarifies the complex relationship that exists between the two modalities: They are indeed linked, but their relationship is more complicated than is suggested by the notion that they are two sides of the same coin.

When Jack isn't Jacques: Simultaneous opposite language-specific speech perceptual learning in French-English bilinguals.

Humans are remarkably good at understanding spoken language, despite the huge variability of the signal as a function of the talker, the situation, and the environment. This success relies on having access to stable representations based on years of speech input, coupled with the ability to adapt to short-term deviations from these norms, e.g. accented speech or speech altered by ambient noise. In the last two decades, there has been a robust research effort focused on a possible mechanism for adjusting to accented speech. In these studies, listeners typically hear 15 - 20 words in which a speech sound has been altered, creating a short-term deviation from its longer-term representation. After exposure to these items, listeners demonstrate "lexically driven phonetic recalibration"-they alter their categorization of speech sounds, expanding a speech category to take into account the recently heard deviations from their long-term representations. In the current study, we investigate such adjustments by bilingual listeners. French-English bilinguals were first exposed to nonstandard pronunciations of a sound (/s/ or /f/) in one language and tested for recalibration in both languages. Then, the exposure continued with both the original type of mispronunciation in the same language, plus mispronunciations in the other language, in the opposite direction. In a final test, we found simultaneous recalibration in opposite directions for the two languages-listeners shifted their French perception in one direction and their English in the other: Bilinguals can maintain separate adjustments, for the same sounds, when a talker's speech differs across two languages.

Common consumer residual insecticides lack efficacy against insecticide-susceptible and resistant populations of the German cockroach (Blattodea: Ectobiidae).

The German cockroach, Blattella germanica (L.) (Blattodea: Ectobiidae), is a ubiquitous pest in affordable housing. They represent a major threat to human health due to their contribution of asthma-exacerbating allergens and the potential to transfer pathogenic microorganisms indoors. Despite well-documented pyrethroid resistance, pyrethroid-based broadcast residual insecticide products are often used by residents to control cockroaches in their homes. Additionally, there is little empirical independent testing of these products. Thus, it remains unclear how effective these commonly used do-it-yourself products are at controlling German cockroaches. This study represents a comprehensive examination of the efficacy of these products with direct, limited, and continuous exposure assays on a variety of common household surfaces on field populations of cockroaches with varying levels of pyrethroid resistance. While most products performed well when applied directly to test insects, mortality was substantially lower across all surfaces with limited exposure (30 min). In continuous exposure assays on a nonporous surface, products took at least 24 hr to cause 100% mortality in a field population, with some products taking up to 5 d to achieve 100% mortality. The findings of this study demonstrate a lack of residual efficacy from common pyrethroid-based consumer-use pesticides products. Given that it is not feasible to find and treat every cockroach in a home directly, the residuality of spray-based formulations is critical for products designed to control German cockroaches. Without residual efficacy, as shown in the consumer aerosol and spray products tested, we expect these products to add little to no value to cockroach control.

Contrast and Complexity in the Low-Temperature Kinetics of CN(v = 1) with O2 and NO: Simultaneous Kinetics and Ringdown in a Uniform Supersonic Flow.

Bimolecular rate coefficients were determined for the reaction CN(v = 1) + NO and O2 using continuous wave cavity ringdown spectroscopy in a uniform supersonic flow (UF-CRDS). The well-matched time scales for ringdown and reaction under pseudo-first-order conditions allow for the use of the SKaR method (simultaneous kinetics and ringdown) in which the full kinetic trace is obtained on each ringdown. The reactions offer an interesting contrast in that the CN(v = 1) + NO system is nonreactive and proceeds by complex-mediated vibrational relaxation, while the CN(v = 1) + O2 reaction is primarily reactive. The measured rate coefficients at 70 K are (2.49 ± 0.08) × 10-11 and (10.49 ± 0.22) × 10-11 cm3 molecule-1 s-1 for the reaction with O2 and NO, respectively. The rate for reaction with O2 is a factor 2 lower than previously reported for v = 0 in the same temperature range, a surprising result, while that for NO is consistent with extrapolation of previous high-temperature measurements to 70 K. The latter is also discussed in light of theoretical calculations and measurements of the rate constants for the association reaction in the high-pressure limit. The measurements are complicated by the presence of a metastable population of high-J CN formed by photolysis of the precursor BrCN, and a kinetic model is developed to treat the competing relaxation and reaction. It is particularly problematic for reactions at low temperatures where the rotational relaxation and reaction have similar rates, precluding a reliable determination of the rate coefficients at 30 K. Also presented are important modifications to the data acquisition and control for the instrument that have yielded considerably enhanced stability and throughput.

Toxicity of cockroach gel baits to the oothecal parasitoid Aprostocetus hagenowii (Hymenoptera: Eulophidae) and implications for cockroach integrated pest management.

Aprostocetus hagenowii (Ratzeburg) is a parasitoid wasp that parasitizes the oothecae of peridomestic pest cockroaches. A. hagenowii has been used in integrated pest management (IPM) programs for cockroach control but little is known about how this parasitoid responds to the insecticides commonly used for cockroach management. Five insecticidal gel bait products containing indoxacarb, clothianidin, fipronil, dinotefuran, or abamectin B1 were tested for their toxicity towards A. hagenowii and the American cockroach, Periplaneta americana (L.; Blattodea: Blattidae), a host of A. hagenowii and a common pest. All baits were tested as fresh and 1-d aged deposits. Indoxacarb was the only active ingredient that did not cause significant (P < 0.05) A. hagenowii mortality compared to the control in both the fresh and aged gel experiments (Median survival time [MST]s: 168 h fresh, 72 h aged). Clothianidin caused the lowest A. hagenowii MSTs across experiments (24 h, fresh and aged). All baits caused significant P. americana mortality as fresh and 1-d aged deposits (P < 0.05). Indoxacarb appears most compatible with A. hagenowii in cockroach IPM.

Parsing Dynamics of Protein Backbone NH and Side-Chain Methyl Groups using Molecular Dynamics Simulations.

Experimental NMR spectroscopy and theoretical molecular dynamics (MD) simulations provide complementary insights into protein conformational dynamics and hence into biological function. The present work describes an extensive set of backbone NH and side-chain methyl group generalized order parameters for the Escherichia coli ribonuclease HI (RNH) enzyme derived from 2-µs microsecond MD simulations using the OPLS4 and AMBER-FF19SB force fields. The simulated generalized order parameters are compared with values derived from NMR 15N and 13CH2D spin relaxation measurements. The squares of the generalized order parameters, S2 for the N-H bond vector and Saxis2 for the methyl group symmetry axis, characterize the equilibrium distribution of vector orientations in a molecular frame of reference. Optimal agreement between simulated and experimental results was obtained by averaging S2 or Saxis2 calculated by dividing the simulated trajectories into 50 ns blocks (∼five times the rotational diffusion correlation time for RNH). With this procedure, the median absolute deviations (MAD) between experimental and simulated values of S2 and Saxis2 are 0.030 (NH) and 0.061 (CH3) for OPLS4 and 0.041 (NH) and 0.078 (CH3) for AMBER-FF19SB. The MAD between OPLS4 and AMBER-FF19SB are 0.021 (NH) and 0.072 (CH3). The generalized order parameters for the methyl group symmetry axis can be decomposed into contributions from backbone fluctuations, between-rotamer dihedral angle transitions, and within-rotamer dihedral angle fluctuations. Analysis of the simulation trajectories shows that (i) backbone and side chain conformational fluctuations exhibit little correlation and that (ii) fluctuations within rotamers are limited and highly uniform with values that depend on the number of dihedral angles considered. Low values of Saxis2, indicative of enhanced side-chain flexibility, result from between-rotamer transitions that can be enhanced by increased local backbone flexibility.

Leveraging Multi-Tissue, Single-Cell Atlases as Tools to Elucidate Shared Mechanisms of Immune-Mediated Inflammatory Diseases.

The observation that certain therapeutic strategies for targeting inflammation benefit patients with distinct immune-mediated inflammatory diseases (IMIDs) is exemplified by the success of TNF blockade in conditions including rheumatoid arthritis, ulcerative colitis, and skin psoriasis, albeit only for subsets of individuals with each condition. This suggests intersecting "nodes" in inflammatory networks at a molecular and cellular level may drive and/or maintain IMIDs, being "shared" between traditionally distinct diagnoses without mapping neatly to a single clinical phenotype. In line with this proposition, integrative tumour tissue analyses in oncology have highlighted novel cell states acting across diverse cancers, with important implications for precision medicine. Drawing upon advances in the oncology field, this narrative review will first summarise learnings from the Human Cell Atlas in health as a platform for interrogating IMID tissues. It will then review cross-disease studies to date that inform this endeavour before considering future directions in the field.

Deuterium spin relaxation of fractionally deuterated ribonuclease H using paired 475 and 950 MHz NMR spectrometers.

Deuterium (2H) spin relaxation of 13CH2D methyl groups has been widely applied to investigate picosecond-to-nanosecond conformational dynamics in proteins by solution-state NMR spectroscopy. The B0 dependence of the 2H spin relaxation rates is represented by a linear relationship between the spectral density function at three discrete frequencies J(0), J(ωD) and J(2ωD). In this study, the linear relation between 2H relaxation rates at B0 fields separated by a factor of two and the interpolation of rates at intermediate frequencies are combined for a more robust approach for spectral density mapping. The general usefulness of the approach is demonstrated on a fractionally deuterated (55%) and alternate 13C-12C labeled sample of E. coli RNase H. Deuterium relaxation rate constants (R1, R1ρ, RQ, RAP) were measured for 57 well-resolved 13CH2D moieties in RNase H at 1H frequencies of 475 MHz, 500 MHz, 900 MHz, and 950 MHz. The spectral density mapping of the 475/950 MHz data combination was performed independently and jointly to validate the expected relationship between data recorded at B0 fields separated by a factor of two. The final analysis was performed by jointly analyzing 475/950 MHz rates with 700 MHz rates interpolated from 500/900 MHz data to yield six J(ωD) values for each methyl peak. The J(ω) profile for each peak was fit to the original (τM, Sf2, τf) or extended model-free function (τM, Sf2, Ss2, τf, τs) to obtain optimized dynamic parameters.

MAPK13 controls structural remodeling and disease after epithelial injury.

All living organisms are charged with repair after injury particularly at epithelial barrier sites, but in some cases this response leads instead to structural remodeling and long-term disease. Identifying the molecular and cellular control of this divergence is key to disease modification. In that regard, stress kinase control of epithelial stem cells is a rational entry point for study. Here we examine the potential for mitogen-activated protein kinase 13 (MAPK13) regulation of epithelial stem cells using models of respiratory viral injury and post-viral lung disease. We show that Mapk13 gene-knockout mice handle acute infectious illness as expected but are protected against structural remodeling manifest as basal-epithelial stem cell (basal-ESC) hyperplasia-metaplasia, immune activation, and mucinous differentiation. In corresponding cell models, Mapk13-deficiency directly attenuates basal-ESC growth and organoid formation. Extension to human studies shows marked induction/activation of basal-cell MAPK13 in clinical samples of comparable remodeling found in asthma and COPD. Here again, MAPK13 gene-knockdown inhibits human basal-ESC growth in culture. Together, the data identify MAPK13 as a control for structural remodeling and disease after epithelial injury and as a suitable target for down-regulation as a disease-modifying strategy.

Monitoring immunE DysregulAtion foLLowing Immune checkpOint-inhibitioN (MEDALLION): protocol for an observational cancer immunotherapy cohort study.

BACKGROUND: Checkpoint inhibitors (CPIs) are widely used in cancer treatment, with transformative impacts on survival. They nonetheless carry a significant risk of toxicity in the form of immune-related adverse events (IrAEs), which may be sustained and life-altering. IrAEs may require high-dose and/or prolonged steroid use and represent a significant healthcare burden. They mimic immune-mediated inflammatory diseases (IMIDs) but understanding of their pathogenesis is limited. The MEDALLION project aims to determine targetable mechanisms of immune dysregulation in IrAE development, employing an immune monitoring approach to determine changes in circulating and tissue resident cells of CPI recipients who do/do not develop them and assessing the contribution of the microbiome in parallel. METHODS: MEDALLION is a non-randomised longitudinal cohort study aiming to recruit 66 cancer patient recipients of anti-PD1/PD-L1, anti-CTLA-4 or combination therapy. Eligible participants include those with malignant melanoma in the adjuvant or metastatic setting, mesothelioma and non-small cell lung carcinoma (NSCLC) treated in the metastatic setting. Comprehensive clinical evaluation is carried out alongside blood, skin swab and stool sampling at the time of CPI initiation (baseline) and during subsequent routine hospital visits on 6 occasions over a 10-month follow-up period. It is conservatively anticipated that one third of enrolled patients will experience a "significant IrAE" (SirAE), defined according to pre-determined criteria specific to the affected tissue/organ system. Those developing such toxicity may optionally undergo a biopsy of affected tissue where appropriate, otherwise being managed according to standard of care. Peripheral blood mononuclear cells will be analysed using multi-parameter flow cytometry to investigate immune subsets, their activation status and cytokine profiles. Stool samples and skin swabs will undergo DNA extraction for 16 S ribosomal RNA (rRNA) sequencing and internal transcribed spacer (ITS) gene sequencing to determine bacterial and fungal microbiome diversity, respectively, including species associated with toxicity. Stored tissue biopsies will be available for in situ and single-cell transcriptomic evaluation. Analysis will focus on the identification of biological predictors and precursors of SirAEs. DISCUSSION: The pathogenesis of IrAEs will be assessed through the MEDALLION cohort, with the potential to develop tools for their prediction and/or strategies for targeted prevention or treatment. TRIAL REGISTRATION: The study was registered on 18/09/2023 in the ISRCTN registry (43,419,676).

Breaking down walls: Continuous potential models for internal motions in NMR spin relaxation.

Simple physical models for restricted diffusion in a potential, which provide important insights for NMR spin relaxation, usually are based on free diffusion within rigid boundaries or diffusion in relatively simple continuous potential energy surfaces. The diffusion-in-a-cone model is an example of the former and diffusion in an N-fold cosine potential is an example of the latter. The present work models restricted diffusion for arbitrary potential energy functions on the surface of a cone or a sphere, by expanding the potentials in Fourier or spherical harmonic series, respectively. The results exhibit simple relationships between generalized order parameters and effective correlation times, critical for analysis of experimental spin relaxation data, and illustrate the transition from diffusive-like to jump-like behavior in multi-well potentials.

Reaction dynamics of S(3P) with 1,3-butadiene and isoprene: crossed-beam scattering, low-temperature flow experiments, and high-level electronic structure calculations.

Sulfur atoms serve as key players in diverse chemical processes, from astrochemistry at very low temperature to combustion at high temperature. Building upon our prior findings, showing cyclization to thiophenes following the reaction of ground-state sulfur atoms with dienes, we here extend this investigation to include many additional reaction products, guided by detailed theoretical predictions. The outcomes highlight the complex formation of products during intersystem crossing (ISC) to the singlet surfaces. Here, we employed crossed-beam velocity map imaging and high-level ab initio methods to explore the reaction of S(3P) with 1,3-butadiene and isoprene under single-collision conditions and in low-temperature flows. For the butadiene reaction, our experimental results show the formation of thiophene via H2 loss, a 2H-thiophenyl radical through H loss, and thioketene through ethene loss at a slightly higher collision energy compared to previous observations. Complementary Chirped-Pulse Fourier-Transform mmWave spectroscopy (CP-FTmmW) measurements in a uniform flow confirmed the formation of thioketene in the reaction at 20 K. For the isoprene reaction, we observed analogous products along with the 2H-thiophenyl radical arising from methyl loss and C3H4S (loss of ethene or H2 + acetylene). CP-FTmmW detected the formation of thioformaldehyde via loss of 1,3-butadiene, again in the 20 K flow. Coupled-cluster calculations on the pathways found by the automated kinetic workflow code KinBot support these findings and indicate ISC to the singlet surface, leading to the generation of various long-lived intermediates, including 5-membered heterocycles.