Lagrangian formulation of nuclear-electronic orbital Ehrenfest dynamics with real-time TDDFT for extended periodic systems.

We present a Lagrangian-based implementation of Ehrenfest dynamics with nuclear-electronic orbital (NEO) theory and real-time time-dependent density functional theory for extended periodic systems. In addition to a quantum dynamical treatment of electrons and selected protons, this approach allows for the classical movement of all other nuclei to be taken into account in simulations of condensed matter systems. Furthermore, we introduce a Lagrangian formulation for the traveling proton basis approach and propose new schemes to enhance its application for extended periodic systems.

New Meroterpenes from South China Sea Soft Coral .

A chemical investigation of the extracts from the soft coral led to the isolation and identification of four new meroterpenes, brassihydroxybenzoquinone A and B ( and ) and brassinaphthoquinone A and B ( and ), along with two known related meroterpenes ( and ). Their structures were elucidated using high-resolution electrospray ionization mass spectrometry (HRESIMS), nuclear magnetic resonance (NMR) spectroscopy, and a comparison with the literature data. All compounds were evaluated for antibacterial activity against six pathogenic bacterial strains and for cytotoxic activity against three cancer cell lines.

Role of UFMylation in tumorigenesis and cancer immunotherapy.

Protein post-translational modifications (PTMs) represent a crucial aspect of cellular regulation, occurring after protein synthesis from mRNA. These modifications, which include phosphorylation, ubiquitination, acetylation, methylation, glycosylation, Sumoylation, and palmitoylation, play pivotal roles in modulating protein function. PTMs influence protein localization, stability, and interactions, thereby orchestrating a variety of cellular processes in response to internal and external stimuli.

Vibrational polaritons with broken in-plane translational symmetry.

Vibrational polaritons form in a planar Fabry-Pérot microcavity when a vibrational mode of a layer of molecules is near resonant with an infrared cavity mode. Here, dispersion relations of vibrational polaritons are studied when the molecular density distribution breaks the macroscopic translational symmetry along the cavity mirror plane. Both perturbative theory and numerical calculations show that, if a homogeneous in-plane molecular distribution is modulated by sinusoidal fluctuations, in addition to a pair of upper and lower polariton branches, a discrete number of side polariton branches may emerge in the polariton dispersion relation.

High throughput mRNA sequencing reveals potential therapeutic targets of Si-Ni-San in the pons for a stress-induced depression model.

Background: An accumulating body of research indicates that the pons is related to the occurrence of depression. Si-Ni-San (SNS) is a well-known Chinese herbal formula that is used to treat depression. Chinese herbal formulae have multiple therapeutic characteristics.

Mesoscale Molecular Simulations of Fabry-Pérot Vibrational Strong Coupling.

Developing theoretical frameworks for vibrational strong coupling (VSC) beyond the single-mode approximation is crucial for a comprehensive understanding of experiments with planar Fabry-Pérot cavities. Herein, a generalized cavity molecular dynamics (CavMD) scheme is developed to simulate VSC of a large ensemble of realistic molecules coupled to an arbitrary 1D or 2D photonic environment. This approach is built upon the Power-Zienau-Woolley Hamiltonian in the normal mode basis and uses a grid representation of the molecular ensembles to reduce the computational cost.

Two swords combination: Smartphone-assisted ratiometric fluorescent and paper sensors for dual-mode detection of glyphosate in edible malt.

The long-term and excessive use of glyphosate (GLY) in diverse matrices has caused serious hazard to the human and environment. However, the ultrasensitive detection of GLY still remains challenging. In this study, the smartphone-assisted dual-signal mode ratiometric fluorescent and paper sensors based on the red-emissive gold nanoclusters (R-AuNCs) and blue-emissive carbon dots (B-CDs) were ingeniously designed accurate and sensitive detection of GLY.

A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations.

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China.

Establishment of a Dual-Signal Enhanced Fluorescent Aptasensor for Highly Sensitive Detection of Ochratoxin A.

A robust and versatile dual-signal enhanced fluorescent aptasensor was developed for ochratoxin A (OTA) detection based on fluorescence resonance energy transfer between 5-carboxyfluorescein (FAM) and Super Green I (SG) fluorophores as the donor and graphene oxide (GO) nanosheet as the acceptor. Abundant SG probes were adsorbed into the FAM-complementary DNA (cDNA)-aptamer double-stranded structure to achieve remarkably enhanced fluorescence responses. Without OTA, the FAM-cDNA-SG conjugates coexisted with GO nanosheets, exhibiting strong fluorescence signals.

New Diterpenes and Diterpene Glycosides with Antibacterial Activity from Soft Coral .

Five new biflorane-type diterpenoids, biofloranates E-I (-), and two new bicyclic diterpene glycosides, lemnaboursides H-I (-), along with the known lemnabourside, were isolated from the South China Sea soft coral . Their chemical structures and stereochemistry were determined based on extensive spectroscopic methods, including time-dependent density functional theory (TDDFT) ECD calculations, as well as a comparison of them with the reported values. The antibacterial activities of the isolated compounds were evaluated against five pathogenic bacteria, and all of these diterpenes and diterpene glycosides showed antibacterial activities against and , with MICs ranging from 4 to 64 µg/mL.

Cyclic peroxides and analogs: Antibacterial, antimalarial, and cytotoxic marine products from Xisha sponge Diacarnus sp.

A chemical investigation of the dichloromethane extract from the Xisha sponge Diacarnus sp. revealed seven undescribed norterpene cyclic peroxides, named diacarperoxides T-Z, and five unreported related norterpenes, named diacarnoids E-I, and eleven previously reported compounds. The structures of these isolated compounds, including their absolute configurations, were elucidated based on extensive spectroscopic analyses, electronic circular dichroism (ECD) calculations, Snatzke's method, [Rh(OCOCF)]-induced ECD spectra, and modified Mosher's method.

Chronic kidney disease and cognitive performance: NHANES 2011-2014.

Purpose: Previous studies suggest an association between chronic kidney disease (CKD) and cognitive impairment. The purpose of this study was to explore the association between the diverse stages of CKD and the cognitive performance of elderly American adults.

Methods: Data from the National Health and Nutrition Examination Survey (NHANES) 2011-2014 were used.

Dynein Light Intermediate Chains Exhibit Different Arginine Methylation Patterns.

Background: The motor protein dynein is integral to retrograde transport along microtubules and interacts with numerous cargoes through the recruitment of cargo-specific adaptor proteins. This interaction is mediated by dynein light intermediate chain subunits LIC1 (DYNC1LI1) and LIC2 (DYNC1LI2), which govern the adaptor binding and are present in distinct dynein complexes with overlapping and unique functions.

Methods: Using bioinformatics, we analyzed the C-terminal domains (CTDs) of LIC1 and LIC2, revealing similar structural features but diverse post-translational modifications (PTMs).

Restraining the power of Proteolysis Targeting Chimeras in the cage: A necessary and important refinement for therapeutic safety.

Proteolysis Targeting Chimeras (PROTACs) represent a significant advancement in therapeutic drug development by leveraging the ubiquitin-proteasome system to enable targeted protein degradation, particularly impacting oncology. This review delves into the various types of PROTACs, such as peptide-based, nucleic acid-based, and small molecule PROTACs, each addressing distinct challenges in protein degradation. It also discusses innovative strategies like bridged PROTACs and conditional switch-activated PROTACs, offering precise targeting of previously "undruggable" proteins.

XIAP-mediated degradation of IFT88 disrupts HSC cilia to stimulate HSC activation and liver fibrosis.

Activation of hepatic stellate cells (HSCs) plays a critical role in liver fibrosis. However, the molecular basis for HSC activation remains poorly understood. Herein, we demonstrate that primary cilia are present on quiescent HSCs but exhibit a significant loss upon HSC activation which correlates with decreased levels of the ciliary protein intraflagellar transport 88 (IFT88).

A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families.

Background: The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck's adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC).

Results: We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data.

Squeezed Protons and Infrared Plasmonic Resonance Energy Transfer.

Unusual nuclear quantum effects may emerge near noble metal nanostructures such as squeezed vibrational states in molecular junctions and plasmonic resonance energy transfer in the infrared domain. Herein, nuclear quantum effects near heavy metals are studied by nuclear-electronic orbital density functional theory (NEO-DFT) with an effective core potential. For a quantum proton sandwiched between a pair of gold tips modeled by two Au clusters, NEO-DFT calculations suggest that the quantum proton density can be squeezed as the tip distance decreases.

First-Principles Approach for Coupled Quantum Dynamics of Electrons and Protons in Heterogeneous Systems.

The coupled quantum dynamics of electrons and protons is ubiquitous in many dynamical processes involving light-matter interaction, such as solar energy conversion in chemical systems and photosynthesis. A first-principles description of such nuclear-electronic quantum dynamics requires not only the time-dependent treatment of nonequilibrium electron dynamics but also that of quantum protons. Quantum mechanical correlation between electrons and protons adds further complexity to such coupled dynamics.

Pathologically relevant aldoses and environmental aldehydes cause cilium disassembly via formyl group-mediated mechanisms.

Carbohydrate metabolism disorders (CMDs), such as diabetes, galactosemia, and mannosidosis, cause ciliopathy-like multiorgan defects. However, the mechanistic link of cilia to CMD complications is still poorly understood. Herein, we describe significant cilium disassembly upon treatment of cells with pathologically relevant aldoses rather than the corresponding sugar alcohols.

Nuclear-Electronic Orbital Quantum Mechanical/Molecular Mechanical Real-Time Dynamics.

Simulating the nuclear-electronic quantum dynamics of large-scale molecular systems in the condensed phase is key for studying biologically and chemically important processes such as proton transfer and proton-coupled electron transfer reactions. Herein, the real-time nuclear-electronic orbital time-dependent density functional theory (RT-NEO-TDDFT) approach is combined with a hybrid quantum mechanical/molecular mechanical (QM/MM) strategy to enable the accurate description of coupled nuclear-electronic quantum dynamics in the presence of heterogeneous environments such as solvent or proteins. The densities of the electrons and quantum protons are propagated in real time, while the other nuclei are propagated classically on the instantaneous electron-proton vibronic surface.

Inhibitory mechanism of KIF3A gene on nasopharyngeal carcinoma stem cells.

To investigate the inhibitory mechanism of the KIF3A gene on nasopharyngeal carcinoma (NPC) tumor stem cells. Set up a blank control group (BCG), NPC group, and KIF3A silence (si-KIF3A) group. The BCG cells were nasopharyngeal normal epithelial cell line NP69, without any treatment, and were cultured routinely; The NPC group cells are human NPC cell line CNE2 cells, which are not subjected to any treatment and are cultured routinely; si-KIF3A group cells were cultured in the offspring of human NPC cell line CNE2 infected with Lentivirus knockdown KIF3A gene.