Generalized Excess Spectroscopy.

With a clear enhancement of the apparent resolution of experimentally determined spectra, excess spectroscopy has been developed as a powerful tool to study solution structures and molecular interactions. In the standard procedure of the method, excess spectra are calculated based on the ideal spectra constructed using two pure compounds. This limits the applications of the method when the pure compounds are unstable or their physical state is different from that of the mixtures. To overcome the problem or to extend the application, we propose generalized excess spectroscopy in this work, where the ideal spectrum is evaluated from the spectra of reference mixtures. After deducing the working equations, we performed digital simulation and then applied the novel approach to a binary system consisting of tert-butanol and carbon tetrachloride. Both results illustrated the feasibility and universality of the method.

Effects of prenatal exposure to persistent organic pollutants on neonatal Outcomes:A mother-child cohort (Shanghai, China).

Persistent organic pollutants (POPs), known as common environmental pollutants, which have adverse effects on neurobehavioral development, are widely applied in industry and agriculture. However, evidence about neurodevelopmental toxicity of POPs in humans is limited. This study aimed to explore the relationship between prenatal exposure to POPs and birth outcome of the newborn including birth length, weight, and head circumference. In this study, 1522 mother-child pairs were included in this study and cord blood samples were collected, which were detected to determine exposure level of 37 POPs in total. After delivery, the neonatal anthropometric indices detection (birth length, weight, and head circumference) was performed. According to the multivariate linear regression, the newborn with high detection rates (≥75 percentile) of hexachlorobenzene (HCB), beta-hexachlorocyclohexane (ß-HCH), p,p'-dichlorodiphenyl dichloroethylene (p,p'-DDE) in the umbilical cord blood were demonstrated negative relationship with birth head circumference after adjusting for confounding factors, but not related with birth length and weight. After confirming that there was a nonlinear relationship between HCB and birth head circumference based on sex stratification through the generalized additive model (GAM), further two-piecewise linear regression model was conducted to explore the saturation threshold effect between HCB and birth head circumference, which showed cord serum HCB concentration greater than 0.5 µg/L was negatively associated with birth head circumference in girls. Our study provided evidence for the adverse influence of HCB, ß-HCH and p,p'-DDE exposure during pregnancy on the birth head circumference of offspring. Although HCB induced reduction of birth head circumference was found in girls, the mechanism of gender difference remained unclear. Further studies are needed to explore the effect of POPs on the growth and development of offspring based on in vivo or in vitro experimental models.

Abnormalities of the Halogen Bonds in the Complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I).

In this work, the hydrogen bonds and halogen bonds in the complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I) have been studied by quantum chemical calculations. We found three interesting abnormalities regarding the interactions. Firstly, the strength of halogen bonds increases in the order of IF < BrF < ClF < F2. Secondly, the halogen bonds formed by F2 are very strong, with an interaction energy in the range between −199.8 and −233.1 kJ/mol. Thirdly, all the halogen bonds are stronger than the hydrogen bonds in the systems we examined. All these results are against the general understanding of halogen bonds. These apparent abnormal properties are reconciled with the high polarizability of the Te atom and the strong inducing effect of F on the Te atom of Y2CTe. These findings provide a new perspective on halogen bonds. Additionally, we also proposed bonding distance-based methods to compare the strength of halogen/hydrogen bonds formed between different donor atoms and the same acceptor atom.

Identification of Essential Sensitive Regions of the Aerolysin Nanopore for Single Oligonucleotide Analysis.

The aerolysin nanopore channel is one of the confined spaces for single molecule analysis which displays high spatial and temporal resolution for the discrimination of single nucleotides, identification of DNA base modification, and analyzing the structural transition of DNAs. However, to overcome the challenge of achieving the ultimate goal of the widespread real analytical application, it is urgent to probe the sensing regions of the aerolysin to further improve the sensitivity. In this paper, we explore the sensing regions of the aerolysin nanopore by a series of well-designed mutant nanopore experiments combined with molecular dynamics simulations-based electrostatic analysis. The positively charged lumen-exposed Lys-238, identified as one of the key sensing sites due to the presence of a deep valley in the electrostatic potentials, was replaced by different charged and sized amino acids. The results show that the translocation time of oligonucleotides through the nanopore can be readily modulated by the choice of the target amino acid at the 238 site. In particular, a 7-fold slower translocation at a voltage bias of +120 mV is observed with respect to the wild-type aerolysin, which provides a high resolution for methylated cytosine discrimination. We further determine that both the electrostatic properties and geometrical structure of the aerolysin nanopore are crucial to its sensing ability. These insights open ways for rationally designing the sensing mechanism of the aerolysin nanopore, thus providing a novel paradigm for nanopore sensing.

Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore.

RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.

Measuring a frequency spectrum for single-molecule interactions with a confined nanopore.

Nanopore analysis is a powerful technique for single molecule analysis by virtue of its electrochemically confined effects. As a single molecule translocates through the nanopore, the featured ionic current pattern on the time scale contains single molecule characteristics including volume, charge, and conformational properties. Although the characteristics of a single molecule in a nanopore have been written to the featured ionic current, extracting the dynamic information from a complex current trace is still a big challenge. Here, we present an applicable nanopore analysis method employing the Hilbert-Huang Transform (HHT) to study the vibrational features and interactions of a single molecule during the dynamic translocation process through the confined space of a nanopore. The HHT method is specially developed for analyzing nonlinear and non-stationary data that is highly compatible with nanopore data with a high frequency resolution. To provide proof-of-concept, we applied HHT to measure the frequency response for the wild-type (WT) aerolysin and mutant K238E aerolysin nanopores with and without the presence of poly(dA)4, respectively. The energy-frequency-time distribution spectra demonstrate that the biological nanopore contributes greatly to the characteristics of the high frequency component (>2 kHz) in the current recording. Our results suggest that poly(dA)4 undergoes relatively more consistent and confined interactions with K238E than WT, leading to a prolonging of the duration time. Therefore, the characteristics in frequency analysis could be regarded as an "single-molecule ionic spectrum" inside the nanopore, which encodes the detailed behaviours of single-molecule weak interactions.

Direct Readout of Single Nucleobase Variations in an Oligonucleotide.

Direct, low-cost, label-free, and enzyme-free identification of single nucleobase is a great challenge for genomic studies. Here, this study reports that wild-type aerolysin can directly identify the difference of four types of single nucleobase (adenine, thymine, cytosine, and guanine) in a free DNA oligomer while avoiding the operations of additional DNA immobilization, adapter incorporation, and the use of the processing enzyme. The nanoconfined space of aerolysin enables DNA molecules to be limited in the narrow pore. Moreover, aerolysin exhibits an unexpected capability of detecting DNA oligomers at the femtomolar concentration. In the future, by virtue of the high sensitivity of aerolysin and its high capture ability for DNA oligomers, aerolysin will play an important role in the studies of single nucleobase variations and open up new avenues for a broad range of nucleic-acid-based sensing and disease diagnosis.

Driven Translocation of Polynucleotides Through an Aerolysin Nanopore.

Aerolysin has been used as a biological nanopore for studying peptides, proteins, and oligosaccharides in the past two decades. Here, we report that wild-type aerolysin could be utilized for polynucleotide analysis. Driven a short polynucleotide of four nucleotides length through aerolysin occludes nearly 50% amplitude of the open pore current. Furthermore, the result of total internal reflection fluorescence measurement provides direct evidence for the driven translocation of single polynucleotide through aerolysin.

In Situ Species Analysis of a Lithium-Ion Battery Electrolyte Containing LiTFSI and Propylene Carbonate.

In this study, we analyzed the species in a model electrolyte consisting of a lithium salt, lithium bis(trifluoromethane sulfone)imide (LiTFSI), and a widely used neutral solvent propylene carbonate (PC) with excess infrared (IR) spectroscopy, ab initio molecular dynamics simulations (AIMD), and quantum chemical calculations. Complexing species including the charged ones [Li+(PC)4, TFSI-, TFSI-(PC), TFSI-(PC)2, and Li(TFSI)2-] are identified in the electrolyte. Quantum chemical calculations show strong Li+···O(PC) interaction, which suggests that Li+ would transport in the mode of solvation-carriage. However, the interaction energy of each hydrogen bond in TFSI-(PC) is very weak, suggesting that TFSI- would transport in hopping mode. In addition, the concentration dependences of the relative population of the species were also derived, providing a scenario for the dissolving process of the salt in PC. These in-depth studies provide physical insights into the structural and interactive properties of the electrolyte of lithium-ion batteries.

Combinatorial expression of γ-protocadherins regulates synaptic connectivity in the mouse neocortex.

In the process of synaptic formation, neurons must not only adhere to specific principles when selecting synaptic partners but also possess mechanisms to avoid undesirable connections. Yet, the strategies employed to prevent unwarranted associations have remained largely unknown. In our study, we have identified the pivotal role of combinatorial clustered protocadherin gamma (γ-PCDH) expression in orchestrating synaptic connectivity in the mouse neocortex. Through 5' end single-cell sequencing, we unveiled the intricate combinatorial expression patterns of γ-PCDH variable isoforms within neocortical neurons. Furthermore, our whole-cell patch-clamp recordings demonstrated that as the similarity in this combinatorial pattern among neurons increased, their synaptic connectivity decreased. Our findings elucidate a sophisticated molecular mechanism governing the construction of neural networks in the mouse neocortex.

Turn on fluorescence detection of curcumin in food matrices by the novel fluorescence sensitizer.

In this study, silane reagents were for the first time explored as the fluorescence sensitizer. They were demonstrated to have fluorescence sensitization effect on curcumin and 3-glycidoxypropyltrimethoxysilane (GPTMS) possessed the strongest effect. Thus, GPTMS was adopted as the novel fluorescence sensitizer to turn on the fluorescence of curcumin by more than two orders of magnitude for detection. In this way, curcumin could be determined with a linear range of 0.2-2000 ng/mL and an LOD of 0.067 ng/mL. The method was applicable to determine curcumin in several actual food samples, which had the good consistency with the high performance liquid chromatographic method, demonstrating the high accuracy of the proposed method. In addition, the curcumins sensitized by GPTMS could be cured under certain conditions and held the potential for solid fluorescence application. This study expanded the scope of fluorescence sensitizer to silane reagents, and provided the novel approach for fluorescence detection of curcumin and further to generate new solid fluorescence system.

Chronic environmental inorganic arsenic exposure causes social behavioral changes in juvenile zebrafish (Danio rerio).

Arsenic (As) is a metalloid commonly found worldwide. Environmental As exposure may cause potential health hazards and behavioral changes in humans and animals. However, the effects of environmental As concentrations on social behavior, especially during the juvenile stage, are unclear. In this study, we observed behavioral changes in juvenile zebrafish after 28 days of exposure to inorganic As (NaAsO2 100 and 500 ppb) in water, especially anxiety and social deficits. Additionally, the level of oxidative stress in the zebrafish brain after As treatment increased, the content of dopamine (DA) decreased, and the transcription level of genes involved in DA metabolism with the activity of monoamine oxidase (MAO) increased. Oxidative stress is a recognized mechanism of nerve damage induced by As exposure. The zebrafish were exposed to N-acetylcysteine (NAC) to reduce As exposure-induced oxidative stress. The results showed improvements in social behavior, DA content, MAO activity, and gene transcription in zebrafish. In conclusion, environmental As exposure can induce behavioral abnormalities, such as anxiety and social deficits in zebrafish, which may be caused by As-induced oxidative stress altering gene transcription levels, causing an increase in MAO activity and a decrease in DA.

Silicon-Carbon Dots-Loaded Mesoporous Silica Nanocomposites (mSiO2@SiCDs): An Efficient Dual Inhibitor of Cu2+-Mediated Oxidative Stress and Aß Aggregation for Alzheimer's Disease.

The redox-active metal ions, especially Cu2+, are highly correlated to Alzheimer's disease (AD) by causing metal ion-mediated oxidative stress and toxic metal-bound ß-amyloid (Aß) aggregates. Numerous pieces of evidence have revealed that the regulation of metal homeostasis could be an effective therapeutic strategy for AD. Herein, in virtue of the interaction of both amino-containing silane and ethylenediaminetetraacetic acid disodium salt for Cu2+, the silicon-carbon dots (SiCDs) are deliberately prepared using these two raw materials as the cocarbon source; meanwhile, to realize the local enrichment of SiCDs and further maximize the chelating ability to Cu2+, the SiCDs are feasibly loaded to the biocompatible mesoporous silica nanoparticles (mSiO2) with the interaction between residual silane groups on SiCDs and silanol groups of mSiO2. Thus-obtained nanocomposites (i.e., mSiO2@SiCDs) could serve as an efficient Cu2+ chelator with satisfactory metal selectivity and further modulate the enzymic activity of free Cu2+ and the Aß42-Cu2+ complex to alleviate the pathological oxidative stress with an anti-inflammatory effect. Besides, mSiO2@SiCDs show an inspiring inhibitory effect on Cu2+-mediated Aß aggregation and further protect the neural cells against the toxic Aß42-Cu2+ complex. Moreover, the transgenic Caenorhabditis elegans CL2120 assay demonstrates the protective efficacy of mSiO2@SiCDs on Cu2+-mediated Aß toxicity in vivo, indicating its potential for AD treatment.

CRH neurons in the lateral hypothalamic area regulate feeding behavior of mice.

Food cues serve as pivotal triggers for eliciting physiological responses that subsequently influence food consumption. The magnitude of response induced by these cues stands as a critical determinant in the context of obesity risk. Nonetheless, the underlying neural mechanism that underpins how cues associated with edible food potentiate feeding behaviors remains uncertain. In this study, we revealed that corticotropin-releasing hormone (CRH)-expressing neurons in the lateral hypothalamic area played a crucial role in promoting consummatory behaviors in mice, shedding light on this intricate process. By employing an array of diverse assays, we initially established the activation of these neurons during feeding. Manipulations using optogenetic and chemogenetic assays revealed that their activation amplified appetite and promoted feeding behaviors, whereas inhibition decreased them. Additionally, our investigation identified downstream targets, including the ventral tegmental area, and underscored the pivotal involvement of the CRH neuropeptide itself in orchestrating this regulatory network. This research casts a clarifying light on the neural mechanism underlying the augmentation of appetite and the facilitation of feeding behaviors in response to food cues. VIDEO ABSTRACT.

Hydrophilic silicon nanoparticles as a turn-off and colorimetric fluorescent probe for curcuminoids detection in food samples and cell imaging.

Hydrophilic fluorescent silicon nanoparticles (SiNPs) with good pH stability, salt-tolerance and anti-photobleaching were for the first time prepared from hydrophobic 3-glycidoxypropyltrimethoxysilane. Employing SiNPs as the fluorescence probe, selective quantification of curcuminoids based on the quenching effect was realized with a linearity of 0.046-7.4 µg/mL and a limit of detection of 17.6 ng/mL. Moreover, in light of fluorescence redshift of SiNPs corresponding to the elevated concentration of curcuminoids, a fluorescence colorimetric method was established based on only one extra probe, i.e. herein SiNPs. Thus, semi-quantification of curcuminoids (0-14.7 µg/mL) was visualized from blue to yellow color. Both the developed quantitative and semi-quantitative probe were successfully applied to determine curcuminoids in various actual food samples. Furthermore, SiNPs possessed low cytotoxicity and succeeded in intracellular curcuminoids imaging. The proposed SiNPs could be a promising fluorescence probe for multiple applications.

Revisiting the Origin of Nanopore Current Blockage for Volume Difference Sensing at the Atomic Level.

Changes in the nanopore ionic current during entry of a target molecule underlie the sensing capability and dominate the intensity and extent of applications of the nanopore approach. The volume exclusion model has been proposed and corrected to describe the nanopore current blockage. However, increasing evidence shows nonconformity with this model, suggesting that the ionic current within a nanopore should be entirely reconsidered. Here, we revisit the origin of nanopore current blockage from a theoretical perspective and propose that the noncovalent interactions between a nanopore and a target molecule affect the conductance of the solution inside the nanopore, leading to enhanced current blockage. Moreover, by considering the example of an aerolysin nanopore discriminating the cytosine DNA and methylcytosine DNA that differ by a single methyl group, we completely demonstrate, by nanopore experiments and molecular dynamics simulations, the essential nature of this noncovalent interaction for discrimination. Our conductance model suggests multiplicative effects of both volume exclusion and noncovalent interaction on the current blockage and provides a new strategy to achieve volume difference sensing at the atomic level with highly specific current events, which would promote the nanopore protein sequencing and its applications in real-life systems.

Unveiling the Heterogenous Dephosphorylation of DNA Using an Aerolysin Nanopore.

The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.

Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface.

DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity.

Single Molecule Study of Hydrogen Bond Interactions Between Single Oligonucleotide and Aerolysin Sensing Interface.

The aerolysin nanopore displays a charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, stronger interaction between the aerolysin nanopore and oligonucleotide represent prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore, and analytes. Taking advantage of site-direct mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such a positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C, and K238Y. As (dA)4 traverses the pores, K238C dramatically produces a six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G, and K238F, our results suggest that the hydrogen bond does not dominate the dynamic translocation process, but enhances the interaction between pores and analytes confined in such nanopore space. These insights give detailed information for the rational design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.

Revealing the transient conformations of a single flavin adenine dinucleotide using an aerolysin nanopore.

Flavin adenine dinucleotide (FAD) as a cofactor is involved in numerous important metabolic pathways where the biological function is intrinsically related to its transient conformations. The confined space of enzymes requires FAD set in its specific intermediate conformation. However, conventional methods only detect stable conformations of FAD molecules, while transient intermediates are hidden in ensemble measurements. There still exists a challenge to uncover the transient conformation of each FAD molecule, which hinders the understanding of the structure-activity relationship of the FAD mechanism. Here, we employ the electrochemically confined space of an aerolysin nanopore to directly characterize a series of transient conformations of every individual FAD. Based on distinguishable current blockages, the "stack", "open", and four quasi-stacked FADs are clearly determined in solution, which is further confirmed by temperature-dependent experiments and mutant aerolysin assay. Combined with molecular dynamics simulations, we achieved a direct correlation between the residual current ratio (I/I 0) and FAD backbone angle. These results would facilitate further understanding of the structure-activity relationship in the flavoprotein.