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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 -
Zhongguo Zhong Yao Za Zhi = Zhongguo... Mar 2024To investigate the quality differences between the seeds and husks of Amomum villosum and explore the rationality of using the seeds without husks, this study determined...
To investigate the quality differences between the seeds and husks of Amomum villosum and explore the rationality of using the seeds without husks, this study determined the content of protocatechuic acid, vanillic acid, epicatechin, quercitrin, volatile oil, water extract, and ethanol extract. The 2,2-diphenyl-1-picrylhydrazyl(DPPH), 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)(ABTS), and hydroxyl radical scavenging activities were determined to evaluate the antioxidant activities of seeds and husks. The quality differences between the seeds and husks were assessed through orthogonal partial least squares-discriminant analysis(OPLS-DA) and analytic hierarchy process(AHP) combined with the entropy weight method(EWM). Significant differences(P<0.05) were observed in all 10 indicators between the seeds and husks. The levels of epicatechin, quercetin, and volatile oil were higher in the seeds, whereas those of protocatechuic acid, vanillic acid, water extract, and ethanol extract were higher in the husks. The seeds showed stronger scavenging ability against DPPH and ABTS radicals, while the husks showed a stronger scavenging effect on hydroxyl radicals. OPLS-DA significantly discriminated between the seeds and husks. Furthermore, volatile oil, water extract, DPPH radical scavenging rate, quercitrin, ABTS radical scavenging rate, hydroxyl radical scavenging rate, and vanillic acid were selected as the main differential indicators by variable importance in projection(VIP). Comprehensive scores calculated by AHP combined with EWM indicated that the seeds were superior to husks in terms of overall quality. However, there are still some dominant components and a certain antioxidant effect in the husks. Therefore, it is suggested to using Amomi Fructus with a certain amount of husks or utilizing the husks for other purposes.
Topics: Amomum; Hydroxyl Radical; Catechin; Vanillic Acid; Antioxidants; Water; Ethanol; Oils, Volatile; Sulfonic Acids; Benzothiazoles; Hydroxybenzoates
PubMed: 38621968
DOI: 10.19540/j.cnki.cjcmm.20231212.102 -
Journal of Chemical Theory and... Apr 2024Over the years, Hedin's self-energy has been proven to be a rather accurate and simple approximation to evaluate electronic quasiparticle energies in solids and in...
Over the years, Hedin's self-energy has been proven to be a rather accurate and simple approximation to evaluate electronic quasiparticle energies in solids and in molecules. Attempts to improve over the simple approximation, the so-called vertex corrections, have been constantly proposed in the literature. Here, we derive, analyze, and benchmark the complete second-order term in the screened Coulomb interaction for finite systems. This self-energy named 32 contains all the possible time orderings that combine 3 Green's functions and 2 dynamic . We present the analytic formula and its imaginary frequency counterpart, with the latter allowing us to treat larger molecules. The accuracy of the 32 self-energy is evaluated on well-established benchmarks (GW100, Acceptor 24, and Core 65) for valence and core quasiparticle energies. Its link with the simpler static approximation, named SOSEX for static screened second-order exchange, is analyzed, which leads us to propose a more consistent approximation named 2SOSEX. In the end, we find that neither the 32 self-energy nor any of the investigated approximations to it improve over one-shot with a good starting point. Only quasi-particle self-consistent HOMO energies are slightly improved by addition of the 32 self-energy correction. We show that this is due to the self-consistent update of the screened Coulomb interaction, leading to an overall sign change of the vertex correction to the frontier quasiparticle energies.
PubMed: 38603811
DOI: 10.1021/acs.jctc.4c00090 -
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 -
Journal of Analytical Toxicology Jun 2024Illicit drug use is a serious and complex public health problem, not only due to the severity of the health damage but also to the social implications, such as...
Illicit drug use is a serious and complex public health problem, not only due to the severity of the health damage but also to the social implications, such as marginalization and drug trafficking. Currently, cocaine (COC) is among the most abused drugs worldwide with about 22 million users. Drug abuse has also been found in women during the pregnancy period, which has shed light on a new group for epidemiology. The diagnosis of COC use in these cases usually depends largely on the mother's reports, which in several cases omit or deny consumption. Therefore, considering physical-chemical methods of sample preparation and exposure biomarkers, the development of analytic toxicological methods can help to confirm drug use during pregnancy. Thus, the objective of the present work was to develop an analytical method based on dispersive liquid-liquid microextraction for the determination of COC analytes, using umbilical cord tissue as an alternative biological matrix, and detection by gas chromatography coupled to mass spectrometry. Therefore, after optimization, the dispersive liquid-liquid microextraction method was fully validated for quantification of COC, benzoylecgonine, cocaethylene, ecgonine, ecgonine methyl ester and norcocaine. The limits of detection were between 15 and 25 ng/g, the limits of quantification were 30 ng/g for ecgonine and 25 ng/g for the other analytes. Linearity ranged from the limits of quantification to 1,000 ng/g. Coefficients of variation for intra-assay precision were <18.5%, inter-assay was <8.75% and bias was <16.4% for all controls. The developed method was applied in 10 suspected positive samples, based on the mother's report and maternal urine screening and confirmation. COC, benzoylecgonine, ecgonine and ecgonine methyl ester were quantified in four umbilical cords with concentrations that ranged from 39.6 to 420.5 ng/g.
Topics: Humans; Liquid Phase Microextraction; Cocaine; Female; Pregnancy; Umbilical Cord; Substance Abuse Detection; Gas Chromatography-Mass Spectrometry; Maternal-Fetal Exchange; Limit of Detection; Reproducibility of Results; Maternal Exposure
PubMed: 38551067
DOI: 10.1093/jat/bkae025 -
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 -
The Journal of Chemical Physics Mar 2024The theory of analytic gradients is presented for the projector-based density functional theory (DFT) embedding approach utilizing the Huzinaga-equation. The advantages...
The theory of analytic gradients is presented for the projector-based density functional theory (DFT) embedding approach utilizing the Huzinaga-equation. The advantages of the Huzinaga-equation-based formulation are demonstrated. In particular, it is shown that the projector employed does not appear in the Lagrangian, and the potential risk of numerical problems is avoided at the evaluation of the gradients. The efficient implementation of the analytic gradient theory is presented for approaches where hybrid DFT, second-order Møller-Plesset perturbation theory, or double hybrid DFT are embedded in lower-level DFT environments. To demonstrate the applicability of the method and to gain insight into its accuracy, it is applied to equilibrium geometry optimizations, transition state searches, and potential energy surface scans. Our results show that bond lengths and angles converge rapidly with the size of the embedded system. While providing structural parameters close to high-level quality for the embedded atoms, the embedding approach has the potential to relax the coordinates of the environment as well. Our demonstrations on a 171-atom zeolite and a 570-atom protein system show that the Huzinaga-equation-based embedding can accelerate (double) hybrid gradient computations by an order of magnitude with sufficient active regions and enables affordable force evaluations or geometry optimizations for molecules of hundreds of atoms.
PubMed: 38530010
DOI: 10.1063/5.0194463 -
Journal of Environmental Management Apr 2024It is challenging to differentiate bacteria residing in the same habitat by direct observation. This difficulty impedes the harvest, application and manipulation of...
It is challenging to differentiate bacteria residing in the same habitat by direct observation. This difficulty impedes the harvest, application and manipulation of functional bacteria in environmental engineering. In this study, we developed a novel method for rapid differentiation of living denitrifying bacteria based on derivative synchronous fluorescence spectroscopy, as exemplified by three heterotrophic nitrification-aerobic denitrification bacteria having the maximum nitrogen removal efficiencies greater than 90%. The intact bacteria and their living surroundings can be analyzed as an integrated target, which eliminates the need for the complex pre-processing of samples. Under the optimal synchronous scanning parameter (Δλ = 40 nm), each bacterium possesses a unique fluorescence spectral structure and the derivative synchronous fluorescence technique can significantly improve the spectral resolution compared to other conventional fluorescence methods, which enables the rapid differentiation of different bacteria through derivative synchronous fluorescence spectra as fast as 2 min per spectrum. Additionally, the derivative synchronous fluorescence technique can extract the spectral signals contributed by bacterial extracellular substances produced in the biological nitrogen removal process. Moreover, the results obtained from our method can reflect the real-time denitrification properties of bacteria in the biological nitrogen removal process of wastewater. All these merits highlight derivative synchronous fluorescence spectroscopy as a promising analytic method in the environmental field.
Topics: Denitrification; Fluorescence; Aerobiosis; Nitrification; Bacteria; Nitrogen; Heterotrophic Processes; Nitrites
PubMed: 38520848
DOI: 10.1016/j.jenvman.2024.120587