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JACS Au Apr 2024We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge...
We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge position provides a qualitative but convenient alternative to the traditional spectroscopic descriptors used to identify oxidation states in these systems, which we demonstrate by providing a calibration curve based on two analytic methods. Furthermore, high energy resolution fluorescence detected XAS (HERFD-XAS) at the S K-edge was used to measure Fe-S bond covalencies and record their variation with the average valence of the Fe atoms. While the Fe-S(thiolate) covalency evolves linearly, gaining 11 ± 0.4% per bond and hole, the Fe-S(μ) covalency evolves asystematically, reflecting changes in the magnetic exchange mechanism. A strong discontinuity manifested for superoxidation to the all-ferric state, distinguishing its electronic structure and its potential (bio)chemical role from those of its redox congeners. We highlight the functional implications of these trends for the reactivity of iron-sulfur cubanes.
PubMed: 38665672
DOI: 10.1021/jacsau.4c00213 -
Global Epidemiology Jun 2024Evidence triangulation may help identify the impact of study design elements on study findings and to tease out biased results when evaluating potential causal...
Evidence triangulation may help identify the impact of study design elements on study findings and to tease out biased results when evaluating potential causal relationships; however, methods for triangulating epidemiologic evidence are evolving and have not been standardized. Building upon key principles of epidemiologic evidence triangulation and risk of bias assessment, and responding to the National Academies of Sciences, Engineering, and Medicine (NASEM) call for applied triangulation examples, the objective of this manuscript is to propose a triangulation framework and to apply it as an illustrative example to epidemiologic studies examining the possible relationship between occupational formaldehyde exposure and risk of myeloid leukemias (ML) including acute (AML) and chronic (CML) types. A nine-component triangulation framework for epidemiological evidence was developed incorporating study quality and ROB guidance from various federal health agencies (i.e., US EPA TSCA and NTP OHAT). Several components of the triangulation framework also drew from widely used epidemiological analytic tools such as stratified meta-analysis and sensitivity analysis. Regarding the applied example, fourteen studies were identified and assessed using the following primary study quality domains to explore potential key sources of bias: 1) study design and analysis; 2) study participation; 3) exposure assessment; 4) outcome assessment; and 5) potential confounding. Across studies, methodological limitations possibly contributing to biased results were observed within most domains. Interestingly, results from one study - often providing the largest and least-precise relative risk estimates, likely reflecting study biases, deviated from most primary study findings indicating no such associations. Triangulation of epidemiological evidence appears to be helpful in exploring inconsistent results for the identification of study results possibly reflecting various biases. Nonetheless, triangulation methodologies require additional development and application to real-world examples to enhance objectivity and reproducibility.
PubMed: 38659700
DOI: 10.1016/j.gloepi.2024.100143 -
Science Advances Apr 2024The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium,...
The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide synthesis under conditions prevailing in space and provide a comprehensive analytic characterization of its products. The application of C allowed us to confirm the suggested pathway of peptide formation that proceeds due to the polymerization of aminoketene molecules that are formed in the C + CO + NH reaction. Here, we address the question of how the efficiency of peptide production is modified by the presence of water molecules. We demonstrate that although water slightly reduces the efficiency of polymerization of aminoketene, it does not prevent the formation of peptides.
Topics: Extraterrestrial Environment; Water; Peptides
PubMed: 38630826
DOI: 10.1126/sciadv.adj7179 -
Communications Biology Apr 2024Trace elements are important for human health but may exert toxic or adverse effects. Mechanisms of uptake, distribution, metabolism, and excretion are partly under...
Trace elements are important for human health but may exert toxic or adverse effects. Mechanisms of uptake, distribution, metabolism, and excretion are partly under genetic control but have not yet been extensively mapped. Here we report a comprehensive multi-element genome-wide association study of 57 essential and non-essential trace elements. We perform genome-wide association meta-analyses of 14 trace elements in up to 6564 Scandinavian whole blood samples, and genome-wide association studies of 43 trace elements in up to 2819 samples measured only in the Trøndelag Health Study (HUNT). We identify 11 novel genetic loci associated with blood concentrations of arsenic, cadmium, manganese, selenium, and zinc in genome-wide association meta-analyses. In HUNT, several genome-wide significant loci are also indicated for other trace elements. Using two-sample Mendelian randomization, we find several indications of weak to moderate effects on health outcomes, the most precise being a weak harmful effect of increased zinc on prostate cancer. However, independent validation is needed. Our current understanding of trace element-associated genetic variants may help establish consequences of trace elements on human health.
Topics: Male; Humans; Trace Elements; Genome-Wide Association Study; Zinc; Selenium; Manganese
PubMed: 38594418
DOI: 10.1038/s42003-024-06101-z -
The Journal of Physical Chemistry... Apr 2024An analytical model of highly nonequilibrium hopping transport of charge carriers in disordered organic semiconductors has been developed. In particular, the initial...
An analytical model of highly nonequilibrium hopping transport of charge carriers in disordered organic semiconductors has been developed. In particular, the initial time interval is considered when transport is controlled by hops down in energy. The model is applied to the calculation of the separation probability of geminate pairs in a semiconductor with a Gaussian energy distribution of localized states. This probability determines the photogeneration efficiency. The temperature dependence of the separation probability is obtained and shown to be much weaker than predicted by the classical Onsager model, in agreement with experiment and Monte Carlo simulations. The field dependence is taken into account using a modified effective temperature method.
PubMed: 38560917
DOI: 10.1021/acs.jpclett.4c00662 -
Small (Weinheim An Der Bergstrasse,... Mar 2024Engineering of catalytically active inorganic nanomaterials holds promising prospects for biomedicine. Catalytically active metal oxides show applications in enhancing...
Engineering of catalytically active inorganic nanomaterials holds promising prospects for biomedicine. Catalytically active metal oxides show applications in enhancing wound healing but have also been employed to induce cell death in photodynamic or radiation therapy. Upon introduction into a biological system, nanomaterials are exposed to complex fluids, causing interaction and adsorption of ions and proteins. While protein corona formation on nanomaterials is acknowledged, its modulation of nanomaterial catalytic efficacy is less understood. In this study, proteomic analyses and nano-analytic methodologies quantify and characterize adsorbed proteins, correlating this protein layer with metal oxide catalytic activity in vitro and in vivo. The protein corona comprises up to 280 different proteins, constituting up to 38% by weight. Enhanced complement factors and other opsonins on nanocatalyst surfaces lead to their uptake into macrophages when applied topically, localizing >99% of the nanomaterials in tissue-resident macrophages. Initially, the formation of the protein corona significantly reduces the nanocatalysts' activity, but this activity can be partially recovered in endosomal conditions due to the proteolytic degradation of the corona. Overall, the research reveals the complex relationship between physisorbed proteins and the catalytic characteristics of specific metal oxide nanoparticles, providing design parameters for optimizing nanocatalysts in complex biological environments.
PubMed: 38556634
DOI: 10.1002/smll.202311115 -
International Journal of Molecular... Mar 2024Inflammatory bowel diseases are extremely common throughout the world. However, in most cases, it is asymptomatic at the initial stage. Therefore, it is important to...
Inflammatory bowel diseases are extremely common throughout the world. However, in most cases, it is asymptomatic at the initial stage. Therefore, it is important to develop non-invasive diagnostic methods that allow identification of the IBD risks in a timely manner. It is well known that gastrointestinal microbiota secrete volatile compounds (VOCs) and their composition may change in IBD. We propose a non-invasive method to identify the dynamics of IBD development in the acute and remission stage at the level of VOCs in model of dextran sulfate sodium (DSS) with chemically induced colitis measured by headspace GC/MS (HS GC/MS). Methods: VOCs profile was identified using a headspace GC/MS (HS GC/MS). GC/MS data were processed using MetaboAnalyst 5.0 and GraphPad Prism 8.0.1 software. The disease activity index (DAI) and histological method were used to assess intestinal inflammation. The peak of intestinal inflammation activity was reached on day 7, according to the disease activity index. Histological examination data showed changes in the intestine due to different stages of inflammation. As the acute inflammation stage was reached, the metabolomic profile also underwent changes, especially at the short-fatty acids level. A higher relative amounts of acetic acid ( value < 0.025) and lower relative amounts of propanoic acid ( value < 0.0005), butanoic acid ( value < 0.005) and phenol 4-methyl- ( value = 0.053) were observed in DSS7 group on day 7 compared to the control group. In remission stage, disease activity indexes decreased, and the histological picture also improved. But metabolome changes continued despite the withdrawal of the DSS examination. A lower relative amounts of propanoic acid ( value < 0.025), butanoic acid ( value < 0.0005), pentanoic acid ( value < 0.0005), and a significant de-crease of hexanoic acid ( value < 0.0005) relative amounts were observed in the DSS14 group compared to the control group on day 14. A model of DSS-induced colitis in rats was successfully implemented for metabolomic assessment of different stages of inflammation. We demonstrated that the ratios of volatile compounds change in response to DSS before the appearance of standard signs of inflammation, determined by DAI and histological examination. Changes in the volatile metabolome persisted even after visual intestine repair and it confirms the high sensitivity of the microbiota to the damaging effects of DSS. The use of HS GC/MS may be an important addition to existing methods for assessing inflammation at early stages.
Topics: Rats; Animals; Mice; Propionates; Gas Chromatography-Mass Spectrometry; Disease Models, Animal; Colitis; Inflammation; Inflammatory Bowel Diseases; Butyrates; Dextran Sulfate; Mice, Inbred C57BL; Colon
PubMed: 38542269
DOI: 10.3390/ijms25063295 -
Advanced Science (Weinheim,... Jun 2024Hexagonal boron nitride (h-BN) is a key ingredient for various 2D van der Waals heterostructure devices, but the exact role of h-BN encapsulation in relation to the...
Hexagonal boron nitride (h-BN) is a key ingredient for various 2D van der Waals heterostructure devices, but the exact role of h-BN encapsulation in relation to the internal defects of 2D semiconductors remains unclear. Here, it is reported that h-BN encapsulation greatly removes the defect-related gap states by stabilizing the chemisorbed oxygen molecules onto the defects of monolayer WS crystals. Electron energy loss spectroscopy (EELS) combined with theoretical analysis clearly confirms that the oxygen molecules are chemisorbed onto the defects of WS crystals and are fixated by h-BN encapsulation, with excluding a possibility of oxygen molecules trapped in bubbles or wrinkles formed at the interface between WS and h-BN. Optical spectroscopic studies show that h-BN encapsulation prevents the desorption of oxygen molecules over various excitation and ambient conditions, resulting in a greatly lowered and stabilized free electron density in monolayer WS crystals. This suppresses the exciton annihilation processes by two orders of magnitude compared to that of bare WS. Furthermore, the valley polarization becomes robust against the various excitation and ambient conditions in the h-BN encapsulated WS crystals.
PubMed: 38493313
DOI: 10.1002/advs.202310197 -
Metabolomics : Official Journal of the... Mar 2024Untargeted direct mass spectrometric analysis of volatile organic compounds has many potential applications across fields such as healthcare and food safety. However,...
INTRODUCTION
Untargeted direct mass spectrometric analysis of volatile organic compounds has many potential applications across fields such as healthcare and food safety. However, robust data processing protocols must be employed to ensure that research is replicable and practical applications can be realised. User-friendly data processing and statistical tools are becoming increasingly available; however, the use of these tools have neither been analysed, nor are they necessarily suited for every data type.
OBJECTIVES
This review aims to analyse data processing and analytic workflows currently in use and examine whether methodological reporting is sufficient to enable replication.
METHODS
Studies identified from Web of Science and Scopus databases were systematically examined against the inclusion criteria. The experimental, data processing, and data analysis workflows were reviewed for the relevant studies.
RESULTS
From 459 studies identified from the databases, a total of 110 met the inclusion criteria. Very few papers provided enough detail to allow all aspects of the methodology to be replicated accurately, with only three meeting previous guidelines for reporting experimental methods. A wide range of data processing methods were used, with only eight papers (7.3%) employing a largely similar workflow where direct comparability was achievable.
CONCLUSIONS
Standardised workflows and reporting systems need to be developed to ensure research in this area is replicable, comparable, and held to a high standard. Thus, allowing the wide-ranging potential applications to be realised.
Topics: Metabolomics; Volatile Organic Compounds; Mass Spectrometry; Reference Standards; Workflow
PubMed: 38491298
DOI: 10.1007/s11306-024-02104-3 -
Molecular & Cellular Proteomics : MCP Apr 2024In recent years, there has been a growing demand for low-input proteomics, particularly in the context of single-cell proteomics (SCP). In this study, we have developed...
In recent years, there has been a growing demand for low-input proteomics, particularly in the context of single-cell proteomics (SCP). In this study, we have developed a lauryl maltose neopentyl glycol (LMNG)-assisted sample preparation (LASP) method. This method effectively reduces protein and peptide loss in samples by incorporating LMNG, a surfactant, into the digestion solution and subsequently removing the LMNG simply via reversed phase solid-phase extraction. The advantage of removing LMNG during sample preparation for general proteomic analysis is the prevention of mass spectrometry (MS) contamination. When we applied the LASP method to the low-input SP3 method and on-bead digestion in coimmunoprecipitation-MS, we observed a significant improvement in the recovery of the digested peptides. Furthermore, we have established a simple and easy sample preparation method for SCP based on the LASP method and identified a median of 1175 proteins from a single HEK239F cell using liquid chromatography (LC)-MS/MS with a throughput of 80 samples per day.
Topics: Maltose; Glycols; Single-Cell Analysis; Proteomics; Analytic Sample Preparation Methods; Humans; HEK293 Cells; Liquid Chromatography-Mass Spectrometry; Immunoprecipitation
PubMed: 38447790
DOI: 10.1016/j.mcpro.2024.100745