Modelling Heterogeneous Anomalous Dynamics of Radiation-Induced Double-Strand Breaks in DNA during Non-Homologous End-Joining Pathway.

The process of end-joining during nonhomologous repair of DNA double-strand breaks (DSBs) after radiation damage is considered. Experimental evidence has revealed that the dynamics of DSB ends exhibit subdiffusive motion rather than simple diffusion with rare directional movement. Traditional models often overlook the rare long-range directed motion. To address this limitation, we present a heterogeneous anomalous diffusion model consisting of subdiffusive fractional Brownian motion interchanged with short periods of long-range movement. Our model sheds light on the underlying mechanisms of heterogeneous diffusion in DSB repair and could be used to quantify the DSB dynamics on a time scale inaccessible to single particle tracking analysis. The model predicts that the long-range movement of DSB ends is responsible for the misrepair of DSBs in the form of dicentric chromosome lesions.

Atomistic simulations for investigation of substrate and salt effects on lipid in-source fragmentation in secondary ion mass spectrometry: A follow-up study.

In-source fragmentation (ISF) poses a significant challenge in secondary ion mass spectrometry (SIMS). These fragment ions increase the spectral complexity and can lead to incorrect annotation of fragments as intact species. The presence of salt that is ubiquitous in biological samples can influence the fragmentation and ionization of analytes in a significant manner, but their influences on SIMS have not been well characterized. To elucidate the effect of substrates and salt on ISF in SIMS, we have employed experimental SIMS in combination with atomistic simulations of a sphingolipid on a gold surface with various NaCl concentrations as a model system. Our results revealed that a combination of bond dissociation energy and binding energy between N-palmitoyl-sphingomyelin and a gold surface is a good predictor of fragment ion intensities in the absence of salt. However, ion-fragment interactions play a significant role in determining fragment yields in the presence of salt. Additionally, the charge distribution on fragment species may be a major contributor to the varying effects of salt on fragmentation. This study demonstrates that atomistic modeling can help predict ionization potential when salts are present, providing insights for more accurate interpretations of complex biological spectra.

Applying Multimodal Mass Spectrometry to Image Tumors Undergoing Ferroptosis Following In Vivo Treatment with a Ferroptosis Inducer.

Epithelial ovarian cancer (EOC) is the most common form of ovarian cancer. The poor prognosis generally associated with this disease has led to the search for improved therapies such as ferroptosis-inducing agents. Ferroptosis is a form of regulated cell death that is dependent on iron and is characterized by lipid peroxidation. Precise mapping of lipids and iron within tumors exposed to ferroptosis-inducing agents may provide insight into processes of ferroptosis in vivo and ultimately assist in the optimal deployment of ferroptosis inducers in cancer therapy. In this work, we present a method for combining matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) with secondary ion mass spectrometry (SIMS) to analyze changes in spatial lipidomics and metal composition, respectively, in ovarian tumors following exposure to a ferroptosis inducer. Tumors were obtained by injecting human ovarian cancer tumor-initiating cells into mice, followed by treatment with the ferroptosis inducer erastin. SIMS imaging detected iron accumulation in the tumor tissue, and sequential MALDI-MS imaging of the same tissue section displayed two chemically distinct regions of lipids. One region was associated with the iron-rich area detected with SIMS, and the other region encompassed the remainder of the tissue section. Bulk lipidomics confirmed the lipid assignments putatively assigned from the MALDI-MS data. Overall, we demonstrate the ability of multimodal MSI to identify the spatial locations of iron and lipids in the same tissue section and associate these regions with clinical pathology.

Fungal organic acid uptake of mineral-derived K is dependent on distance from carbon hotspot.

IMPORTANCE: Fungal species are foundational members of soil ecosystems with vital contributions that support interspecies resource translocation. The minute details of these biogeochemical processes are poorly investigated. Here, we addressed this knowledge gap by probing fungal growth in a novel mineral-doped soil micromodel platform using spatially-resolved imaging methodologies. We found that fungi uptake K from K-rich minerals using organic acids exuded in a distance-dependent manner from a carbon-rich hotspot. While identification of specific mechanisms within soil remains challenging, our findings demonstrate the significance of reduced complexity platforms such as the mineral-doped micromodel in probing biogeochemical processes. These findings provide visualization into hyphal uptake and transport of mineral-derived nutrients in a resource-limited environment.

Design of the elusive proteinaceous oxygen donor copper site suggests a promising future for copper for MRI contrast agents.

We report the preparation and spectroscopic characterization of a highly elusive copper site bound exclusively to oxygen donor atoms within a protein scaffold. Despite copper generally being considered unsuitable for use in MRI contrast agents, which in the clinic are largely Gd(III) based, the designed copper coiled coil displays relaxivity values equal to, or superior than, those of the Gd(III) analog at clinical field strengths. The creation of this new-to-biology proteinaceous CuOx-binding site demonstrates the power of the de novo peptide design approach to access chemistry for abiological applications, such as for the development of MRI contrast agents.

Atomistic simulations for investigation of substrate effects on lipid in-source fragmentation in secondary ion mass spectrometry.

In beam-based ionization methods, the substrate plays an important role on the desorption mechanism of molecules from surfaces. Both the specific orientation that a molecule adopts at a surface and the strength of the molecule-surface interaction can greatly influence desorption processes, which in turn will affect the ion yield and the degree of in-source fragmentation of a molecule. In the beam-based method of secondary ion mass spectrometry (SIMS), in-source fragmentation can be significant and molecule specific due to the hard ionization method of using a primary ion beam for molecule desorption. To investigate the role of the substrate on orientation and in-source fragmentation, we have used atomistic simulations-molecular dynamics in combination with density functional theory calculations-to explore the desorption of a sphingolipid (palmitoylsphingomyelin) from a model surface (gold). We then compare SIMS data from this model system to our modeling findings. Using this approach, we found that the combined adsorption and binding energy of certain bonds associated with the headgroup fragments (C3H8N+, C5H12N+, C5H14NO+, and C5H15PNO4 +) was a good predictor for fragment intensities (as indicated by relative ion yields). This is the first example where atomistic simulations have been applied in beam-based ionization of lipids, and it presents a new approach to study biointerfacial lipid ordering effects on SIMS imaging.

Medical morbidity and risk of general hospital admission associated with concurrent anorexia nervosa and COVID-19: An observational study.

OBJECTIVE: Investigate medical morbidity and risk of general hospital admission for patients with concurrent coronavirus disease 2019 (COVID-19) and anorexia nervosa (AN) who have not received severe acute respiratory syndrome coronavirus 2 vaccination. METHODS: United Kingdom eating disorders clinicians contributed to a database of patients with an eating disorder and COVID-19. We used this to investigate demography, symptoms, hospitalization, treatment, and outcomes for those with AN. RESULTS: We describe data for 49 patients (median age 21.5 years [interquartile range 17.0-33.5], 46 female) including 36 adults and 13 under-18-year-olds. Three (6.1% [95% confidence interval 1.3%-17.9]) were admitted to a general hospital. For this sample, the expected age-standardized hospital admission rate per COVID-19 case (based on the general population of England) was 2.6% and therefore not significantly different to the hospitalization rate we observed. Three (including two of those admitted to hospital) contracted pneumonia. One had severe pneumonia and was admitted to an intensive care unit. No deaths or use of mechanical ventilation were recorded. DISCUSSION: To our knowledge, this represents the first study investigating medical morbidity or frequency of hospitalization for patients with COVID-19 and AN. We did not find evidence that patients with AN are at increased risk of severe COVID-19. PUBLIC SIGNIFICANCE: Medical morbidity and risk of hospitalization associated with concurrent COVID-19 and anorexia nervosa (AN) had not, to our knowledge, been studied before. We used a database of patients with eating disorders and COVID-19 (to which United Kingdom clinicians had contributed) to investigate presentation, treatment, outcomes, and COVID-19 severity for those with AN and COVID-19. We did not find evidence that patients with AN are at increased risk of severe COVID-19.

Neural networks in pulsed dipolar spectroscopy: A practical guide.

This is a methodological guide to the use of deep neural networks in the processing of pulsed dipolar spectroscopy (PDS) data encountered in structural biology, organic photovoltaics, photosynthesis research, and other domains featuring long-lived radical pairs and paramagnetic metal ions. PDS uses distance dependence of magnetic dipolar interactions; measuring a single well-defined distance is straightforward, but extracting distance distributions is a hard and mathematically ill-posed problem requiring careful regularisation and background fitting. Neural networks do this exceptionally well, but their "robust black box" reputation hides the complexity of their design and training - particularly when the training dataset is effectively infinite. The objective of this paper is to give insight into training against simulated databases, to discuss network architecture choices, to describe options for handling DEER (double electron-electron resonance) and RIDME (relaxation-induced dipolar modulation enhancement) experiments, and to provide a practical data processing flowchart.

Discovery of Reversible Covalent Bruton's Tyrosine Kinase Inhibitors PRN473 and PRN1008 (Rilzabrutinib).

Bruton's tyrosine kinase (BTK), a Tec family tyrosine kinase, is critical in immune pathways as an essential intracellular signaling element, participating in both adaptive and immune responses. Currently approved BTK inhibitors are irreversible covalent inhibitors and limited to oncology indications. Herein, we describe the design of covalent reversible BTK inhibitors and the discoveries of PRN473 (11) and rilzabrutinib (PRN1008, 12). These compounds have exhibited potent and durable inhibition of BTK, in vivo efficacy in rodent arthritis models, and clinical efficacy in canine pemphigus foliaceus. Compound 11 has completed phase 1 trials as a topical agent, and 12 is in phase 3 trials for pemphigus vulgaris and immune thrombocytopenia.

Estimating the percentage of patients who might benefit from proton beam therapy instead of X-ray radiotherapy.

OBJECTIVES: High-energy Proton Beam Therapy (PBT) commenced in England in 2018 and NHS England commissions PBT for 1.5% of patients receiving radical radiotherapy. We sought expert opinion on the level of provision. METHODS: Invitations were sent to 41 colleagues working in PBT, most at one UK centre, to contribute by completing a spreadsheet. 39 responded: 23 (59%) completed the spreadsheet; 16 (41%) declined, arguing that clinical outcome data are lacking, but joined six additional site-specialist oncologists for two consensus meetings. The spreadsheet was pre-populated with incidence data from Cancer Research UK and radiotherapy use data from the National Cancer Registration and Analysis Service. 'Mechanisms of Benefit' of reduced growth impairment, reduced toxicity, dose escalation and reduced second cancer risk were examined. RESULTS: The most reliable figure for percentage of radical radiotherapy patients likely to benefit from PBT was that agreed by 95% of the 23 respondents at 4.3%, slightly larger than current provision. The median was 15% (range 4-92%) and consensus median 13%. The biggest estimated potential benefit was from reducing toxicity, median benefit to 15% (range 4-92%), followed by dose escalation median 3% (range 0 to 47%); consensus values were 12 and 3%. Reduced growth impairment and reduced second cancer risk were calculated to benefit 0.5% and 0.1%. CONCLUSIONS: The most secure estimate of percentage benefit was 4.3% but insufficient clinical outcome data exist for confident estimates. The study supports the NHS approach of using the evidence base and developing it through randomised trials, non-randomised studies and outcomes tracking. ADVANCES IN KNOWLEDGE: Less is known about the percentage of patients who may benefit from PBT than is generally acknowledged. Expert opinion varies widely. Insufficient clinical outcome data exist to provide robust estimates. Considerable further work is needed to address this, including international collaboration; much is already underway but will take time to provide mature data.

Survey of the publics' preferences for communication of medical radiation risk.

To comply with the Ionising Radiations (Medical Exposures) Regulations 2017, patients need to be adequately informed of medical radiation risks prior to exposure. This study used a survey developed in partnership with patients and members of the public to explore patient preferences for radiation risk communication. It was distributed through social media between 28/4/2020 and 18/7/2020. All respondents (N= 376) wanted to be informed about radiation risk, though the threshold at which they wished to be informed varied. The current practice of displaying posters in waiting areas does not meet the expressed preference of the patients if used in isolation. Only 6% of respondents were satisfied with the commonly used statement that the 'risk is low' if used in isolation. The majority of respondents (73%) said they would not be concerned about an increase in the risk of cancer of less than 1 in 10 000. The level of risk at which patients express a concern and the methodology for risk communication has been evaluated and based on these findings, and pre-existing literature, a graded approach to radiation risk communication based on modality is proposed. Patients must be involved throughout the evolution of this practice.

The role of antifreeze glycoprotein (AFGP) and polyvinyl alcohol/polyglycerol (X/Z-1000) as ice modulators during partial freezing of rat livers.

Introduction: The current liver organ shortage has pushed the field of transplantation to develop new methods to prolong the preservation time of livers from the current clinical standard of static cold storage. Our approach, termed partial freezing, aims to induce a thermodynamically stable frozen state at high subzero storage temperatures (-10°C to -15°C), while simultaneously maintaining a sufficient unfrozen fraction to limit ice-mediated injury. Methods and results: Using glycerol as the main permeating cryoprotectant agent, this research first demonstrated that partially frozen rat livers showed similar outcomes after thawing from either -10°C or -15°C with respect to subnormothermic machine perfusion metrics. Next, we assessed the effect of adding ice modulators, including antifreeze glycoprotein (AFGP) or a polyvinyl alcohol/polyglycerol combination (X/Z-1000), on the viability and structural integrity of partially frozen rat livers compared to glycerol-only control livers. Results showed that AFGP livers had high levels of ATP and the least edema but suffered from significant endothelial cell damage. X/Z-1000 livers had the highest levels of ATP and energy charge (EC) but also demonstrated endothelial damage and post-thaw edema. Glycerol-only control livers exhibited the least DNA damage on Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining but also had the lowest levels of ATP and EC. Discussion: Further research is necessary to optimize the ideal ice modulator cocktail for our partial-freezing protocol. Modifications to cryoprotective agent (CPA) combinations, including testing additional ice modulators, can help improve the viability of these partially frozen organs.

Versatile Para-Substituted Pyridine Lanthanide Coordination Complexes Allow Late Stage Tailoring of Complex Function.

A series of cationic and neutral p-Br and p-NO2 pyridine substituted Eu(III) and Gd(III) coordination complexes serve as versatile synthetic intermediates. Nucleophilic aromatic substitution occurs readily at the para position under mild conditions, allowing C-N and C-C bond forming reactions to take place, permitting the introduction of azide, amino and alkynyl substituents. For Eu(III) complexes, this approach allows late stage tuning of absorption and emission spectral properties, exemplified by the lowering of the energy of an LMCT transition accompanied by a reduction in the Eu-Npy bond length. Additionally, these complexes provide direct access to the corresponding Eu(II) analogues. With the Gd(III) series, the nature of the p-substituent does not significantly change the EPR properties (linewidth, relaxation times), as required for their development as EPR spin probes that can be readily conjugated to biomolecules under mild conditions.

Ambient Single-Cell Analysis and Native Tissue Imaging Using Laser-Ablation Electrospray Ionization Mass Spectrometry with Increased Spatial Resolution.

Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is an emerging method that has the potential to transform the field of metabolomics. This is in part due to LAESI-MS being an ambient ionization method that requires minimal sample preparation and uses (endogenous) water for in situ analysis. This application note details the employment of the "LAESI microscope" source to perform spatially resolved MS analysis of cells and MS imaging (MSI) of tissues at high spatial resolution. This source configuration utilizes a long-working-distance reflective objective that permits both visualization of the sample and a smaller LAESI laser beam profile than conventional LAESI setups. Here, we analyzed 200 single cells of Allium cepa (red onion) and imaged Fittonia argyroneura (nerve plant) in high spatial resolution using this source coupled to a Fourier transform mass spectrometer for high-mass-resolution and high-mass-accuracy metabolomics.

Optical Microscopy-Guided Laser Ablation Electrospray Ionization Ion Mobility Mass Spectrometry: Ambient Single Cell Metabolomics with Increased Confidence in Molecular Identification.

Single cell analysis is a field of increasing interest as new tools are continually being developed to understand intercellular differences within large cell populations. Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is an emerging technique for single cell metabolomics. Over the years, it has been validated that this ionization technique is advantageous for probing the molecular content of individual cells in situ. Here, we report the integration of a microscope into the optical train of the LAESI source to allow for visually informed ambient in situ single cell analysis. Additionally, we have coupled this 'LAESI microscope' to a drift-tube ion mobility mass spectrometer to enable separation of isobaric species and allow for the determination of ion collision cross sections in conjunction with accurate mass measurements. This combined information helps provide higher confidence for structural assignment of molecules ablated from single cells. Here, we show that this system enables the analysis of the metabolite content of Allium cepa epidermal cells with high confidence structural identification together with their spatial locations within a tissue.

Testing a multicomponent lifestyle intervention for combatting childhood obesity.

BACKGROUND: Childhood obesity is a major global health concern. Weight-management camps involving delivery of a program of physical activity, health education, and healthy eating are an effective treatment, although post-intervention weight-management is less well understood. Our objective was to assess the effectiveness of a weight-management camp followed by a community intervention in supporting weight-management for overweight children and children with obesity. METHODS: Participants were overweight Qatari schoolchildren or schoolchildren with obesity, ages 8-14 years, (n = 300) recruited over a three-year period across 14 randomly selected schools in the Doha area. They attended a two-week weight management camp, then a 10-week program of weekly lifestyle education and physical activity sessions, which also included behavior change techniques. The programme was cognitive behavioural therapy (CBT)-focused with a strong element of behavioural economics blended in. RESULTS: Participants saw a significant BMI SDS reduction as a result of the entire intervention (camp + education and activity sessions) both at the individual (p < 0.0001) and cluster/school (p = 0.0002) levels, and weight loss occurred during each intervention stage separately for the camp (p < 0.0001 for both the individual and cluster/school levels) and the lifestyle education and activity phase (p < 0.0001 and p = 0.0220 at the individual and cluster/school levels, respectively). CONCLUSIONS: Weekly lifestyle education and activity sessions which include behavior change techniques may be useful in promoting continued weight management in the period following intensive, immersive childhood obesity interventions. TRIAL REGISTRATION: ClinicalTrials.gov NCT02972164 , November 23, 2016.

Cloud Formation From a Localized Water Release in the Upper Mesosphere: Indication of Rapid Cooling.

Polar mesospheric clouds (PMCs) occur in the summer near 82 -85km altitude due to seasonal changes of temperature and humidity. However, water vapor and associated PMCs have also been observed associated with rocket exhaust. The effects of this rocket exhaust on the temperature of the upper mesosphere are not well understood. To investigate these effects, 220 kg of pure water was explosively released at 85 km as part of the Super Soaker sounding rocket experiment on the night of January 25-26, 2018 at Poker Flat Research Range (65°N, 147°W). A cloud formed within 18 s and was measured by a ground-based Rayleigh lidar. The peak altitude of the cloud appeared to descend from 92 to 78 km over 3 min. Temperatures leading up to the release were between 197 and 232 K, about 50 K above the summertime water frost point when PMCs typically occur. The apparent motion of the cloud is interpreted in terms of the expansion of the explosive release. Analysis using a water vapor radiative cooling code coupled to a microphysical model indicates that the cloud formed due to the combined effects of rapid radiative cooling (∼25 K) by meter-scale filaments of nearly pure water vapor (∼1 ppv) and an increase in the frost point temperature (from 150 to 200 K) due to the high concentration of water vapor. These results indicate that water exhaust not only acts as a reservoir for mesospheric cloud production but also actively cools the mesosphere to induce cloud formation.

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics.

Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.

Collybistin SH3-protein isoforms are expressed in the rat brain promoting gephyrin and GABA-A receptor clustering at GABAergic synapses.

Collybistin (CB) is a guanine nucleotide exchange factor (GEF) selectively localized at GABAergic and glycinergic postsynapses. Analysis of mRNA shows that several isoforms of collybistin are expressed in the brain. Some of the isoforms have a SH3 domain (CBSH3+) and some have no SH3 domain (CBSH3-). The CBSH3+ mRNAs are predominantly expressed over CBSH3-. However, in an immunoblot study of mouse brain homogenates, only CBSH3+ protein isoforms were detected, proposing that CBSH3- protein might not be expressed in the brain. The expression or lack of expression of CBSH3- protein is an important issue because CBSH3- has a strong effect in promoting the postsynaptic clustering of gephyrin and GABA-A receptors (GABAA Rs). Moreover CBSH3- is constitutively active; therefore lower expression of CBSH3- protein might play a relatively stronger functional role than the more abundant but self-inhibited CBSH3+ isoforms, which need to be activated. We are now showing that: (a) CBSH3- protein is expressed in the brain; (b) parvalbumin positive (PV+) interneurons show higher expression of CBSH3- protein than other neurons; (c) CBSH3- is associated with GABAergic synapses in various regions of the brain and (d) knocking down CBSH3- in hippocampal neurons decreases the synaptic clustering of gephyrin and GABAA Rs. The results show that CBSH3- protein is expressed in the brain and that it plays a significant role in the size regulation of the GABAergic postsynapse.

Use of a deactivated PTV injector liner and GCMS/MS for the quantitative determination of multiple pesticide residues in fruit and vegetables.

The quantitative determination of multiple pesticide residues in food is an iterative process given the frequent changes in monitoring specifications set by regulatory authorities, introduction of new pesticide active ingredients, variety of commodities encountered and advances in the capability of analytical instrumentation and software platforms. The method described here:•replaces our previous methodology [1] that was based on an ethyl acetate extraction [2], two different sample extract clean-up regimes depending on the commodity; either Gel Permeation Chromatography (GPC) or Solid Phase Extraction (SPE) and GC/MSMS analysis using cool on-column injection and permits higher throughput using the same QuEChERS extraction method used for LCMS/MS analysis [3]•uses PTV injection incorporating a deactivated (baffled) injection liner required to improve performance for 'difficult to analyse' pesticides e.g. captan, dichlofluanid, folpet, tolylfluanid.•has been validated for the quantitative determination of 113 different pesticides and their metabolites in a range of fruit and vegetables of high water content and high acid and high water content i.e. cabbage, lemon, pepper, plum and spinach and complies with requirements of European Commission guidance document on Analytical Quality Control and Method Validation Procedures for Pesticides Residues Analysis in food and feed - SANTE/12682/2019 [4].