A New Structure Feature Introduced to Predict Protein-Protein Interaction Sites.

Interaction between proteins often depends on the sequence features and structure features of proteins. Both of these features are helpful for machine learning methods to predict (protein-protein interaction) PPI sites. In this study, we introduced a new structure feature: concave-convex feature on the protein surface, which was computed by the structural data of proteins in Protein Data Bank database.

Geographical distribution and evolutionary dynamics of H4Nx avian influenza viruses.

H4Nx avian influenza viruses (AIVs) have been isolated from wild birds and poultry and can also cross the species barrier to infect mammals (pigs and muskrats). The widespread presence of these viruses in wild birds and poultry and their ability to be transmitted interspecies make them an undeniable hazard to the poultry farming industry. In the present study, we collected fecal and swab samples from wild birds and poultry in Guangdong Province from January 2019 to March 2024, and various subtypes of AIVs were isolated, including 19 strains of H4 subtype AIVs.

The first emergence of paramyxovirus type 12 in wild birds in mainland, China.

Avian paramyxoviruses (APMV) belong to the subfamily Avulavirinae of the family Paramyxoviridae and include 22 distinct subtypes or serotypes (1-22). Avian paramyxovirus serotype 12 (APMV-12) is found sporadically in wild birds worldwide, and reports from only Italy and Taiwan have been published to date; information on its genetic variation and biological characteristics is still limited. In this study, 3 APMV-12 strains, designated WB19, LY9, and LY11, were isolated from 8643 wild bird faecal samples during the annual influenza virus surveillance of wild birds in Guangdong, China between 2018 and 2024, which is first reported in mainland China.

Biogeographic and co-occurrence network differentiation of fungal communities in warm-temperate montane soils.

Studying the biogeographic patterns of fungal communities across altitudinal and soil depth gradients is essential for understanding how environmental variations shape the diversity and functionality of these complex ecological assemblages. Here, we evaluated the response and assembly patterns of fungal communities to altitude and soil depth, and the co-occurrence patterns influencing soil fungal metabolic preferences on Dongling Mountain. We observed significant variations in fungal β-diversity, driven by elevation and soil depth, with climatic parameters (MAT and MAP) and nutrient concentrations (TOC, TP, and TN) serving as prominent influencers.

Polymer-DNA Carriers Co-Deliver Photosensitizer and siRNA for Light-Promoted Gene Transfection and Hypoxia-Relieved Photodynamic Therapy.

Photochemical internalization is an efficient strategy relying on photodynamic reactions to promote siRNA endosomal escape for the success of RNA-interference gene regulation, which makes gene-photodynamic combined therapy highly synergistic and efficient. However, it is still desired to explore capable carriers to improve the delivery efficiency of the immiscible siRNA and organic photosensitizers simultaneously. Herein, we employ a micellar nanostructure (PSNA) self-assembled from polymer-DNA molecular chimeras to fulfill this task.

Biologically produced and metal-organic framework delivered dual-cut CRISPR/Cas9 system for efficient gene editing and sensitized cancer therapy.

Manipulation of the lactate metabolism is an efficient way for cancer treatment given its involvement in cancer development, metastasis, and immune escape. However, most of the inhibitors of lactate transport carriers suffer from poor specificity. Herein, we use the CRISPR/Cas9 system to precisely downregulate the monocarboxylate carrier 1 (MCT1) expression.

Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China.

Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain.

The Impact and Determinants of Mountainous Topographical Factors on Soil Microbial Community Characteristics.

Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation affect soil physicochemical properties, soil microbial communities, and their contributing factors.

Bromine Substitution Improves the Photothermal Performance of π-Conjugated Phototheranostic Molecules.

NIR-II fluorescence imaging-guided photothermal therapy (PTT) has been widely investigated due to its great application potential in tumor theranostics. PTT is an effective and non-invasive tumor treatment method that can adapt to tumor hypoxia; nevertheless, simple and effective strategies are still desired to develop new materials with excellent PTT properties to meet clinical requirements. In this work, we developed a bromine-substitution strategy to enhance the PTT of A-D-A'-D-A π-conjugated molecules.

Ultra-stable MOF@MOF nanoplatform for photodynamic therapy sensitized by relieved hypoxia due to mitochondrial respiration inhibition.

Metal-organic frameworks (MOFs) with periodically arranged porphyrinic linkers avoiding the self-quenching issue of porphyrins in photodynamic therapy (PDT) have been widely applied. However, the porphyrinic MOFs still face challenges of poor stability under physiological conditions and limited photodynamic efficiency by the hypoxia condition of tumors. Herein, we fabricate the MOF@MOF structure with a protective MOF shell to improve the stability and relieve the hypoxia condition of tumors for sensitized PDT.

One-Pot Rapid Synthesis of Cu-Doped GOD@MOF to Amplify the Antitumor Efficacy of Chemodynamic Therapy.

Chemodynamic therapy (CDT) relies on the transformation of intracellular hydrogen peroxide (HO) to hydroxyl radicals (·OH) with higher toxicity under the catalysis of Fenton/Fenton-like reagents, which amplifies the oxidative stress and induces significant cellular apoptosis. However, the CDT efficacy is generally limited by the overexpressed GSH and insufficient endogenous HO in tumors. Co-delivery of Cu and glucose oxidase (GOD) can lead to a Cu/Cu circulation to realize GSH depletion and amplify the Fenton-like reaction.

NIR-II Luminescent and Multi-Responsive Rare Earth Nanocrystals for Improved Chemodynamic Therapy.

Chemodynamic therapy (CDT) based on the Fe-mediated Fenton reaction can amplify intracellular oxidative stress by producing toxic •OH. However, the high-dose need for Fe delivery in tumors and its significant cytotoxicity to normal tissues set a challenge. Therefore, a controllable delivery to activate the Fenton reaction and enhance Fe tumor accumulation has become an approach to solve this conflict.

Inhibitory effect of ficin on Candida albicans biofilm formation and pre-formed biofilms.

Background: To investigate the effect of ficin, a type of proteases, on Candida albicans (C. albicans) biofilm, including forming and pre-formed biofilms.

Methods: Crystal violet tests together with colony forming unit (CFU) counts were used to detect fungal biofilm biomass.

Iron Hydroxide/Oxide-Reduced Graphene Oxide Nanocomposite for Dual-Modality Photodynamic and Photothermal Therapy In Vitro and In Vivo.

Minimal invasive phototherapy utilising near-infrared (NIR) laser to generate local reactive oxygen species (ROS) and heat has few associated side effects and is a precise treatment in cancer therapy. However, high-efficiency and safe phototherapeutic tumour agents still need developing. The application of iron hydroxide/oxide immobilised on reduced graphene oxide (FeOxH-rGO) nanocomposites as a therapeutic agent in integration photodynamic cancer therapy (PDT) and photothermal cancer therapy (PTT) was discussed.

Advanced Cancer Starvation Therapy by Simultaneous Deprivation of Lactate and Glucose Using a MOF Nanoplatform.

Recent investigations reveal that lactate is not a waste product but a major energy source for cells, especially in the mitochondria, which can support cellular survival under glucose shortage. Accordingly, the new understanding of lactate prompts to target it together with glucose to pursue a more efficient cancer starvation therapy. Herein, zeolitic imidazolate framework-8 (ZIF-8) nanoplatforms are used to co-deliver α-cyano-4-hydroxycinnamate (CHC) and glucose oxidase (GOx) and fulfill the task of simultaneous depriving of lactate and glucose, resulting in a new nanomedicine CHC/GOx@ZIF-8.

GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions.

Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data. With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples, a user-friendly database making efficient reuse of these important resources is needed. Here, we use the genomes of 208 modern domestic goats, 24 bezoars, 46 wild ibexes, and 82 ancient goats to present a comprehensive goat genome variation database (GGVD).

DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion.

Alternative splicing enables a gene translating into different isoforms and into the corresponding proteoforms, which actually accomplish various biological functions of a living body. Isoform-isoform interactions (IIIs) provide a higher resolution interactome to explore the cellular processes and disease mechanisms than the canonically studied protein-protein interactions (PPIs), which are often recorded at the coarse gene level. The knowledge of IIIs is critical to map pathways, understand protein complexity and functional diversity, but the known IIIs are very scanty.

Mn-DNA coordination of nanoparticles for efficient chemodynamic therapy.

A kind of nanoparticle is developed for highly efficient chemodynamic therapy that only relies on the endogenous H2O2 of cancer cells. For this nanoparticle, high-molecular-weight DNA is used as the biocompatible carrier to load abundant Mn2+ ions. Therefore, the resultant Mn-DNA coordination nanoparticles can efficiently deliver and sensitively release Mn2+ in cancer cells, resulting in high toxicity through the Fenton-like reaction.

An atlas of CNV maps in cattle, goat and sheep.

Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations.

Utilizing Polymer Micelle to Control Dye J-aggregation and Enhance Its Theranostic Capability.

We utilize polymer micelle to precisely control indocyanine green (ICG) J-aggregation in a fast and highly efficient way. In addition to simple encapsulation, the polymer micelle plays a role as a host template to drive ICG J-aggregation by the synergy of electrostatic and hydrophobic attractions. We further demonstrate that, due to the robust host-guest interaction, the intact of ICG J-aggregate will be secured by the polymer encapsulation during the intracellular and in vivo incubation.

Enzymatically Synthesized DNA Polymer as Co-carrier for Enhanced RNA Interference.

Polymerization of small interfering RNA (siRNA) has been demonstrated as a promising strategy to improve siRNA delivery, which will change the low-charge and rigid properties of single siRNA and enhance its electrostatic interactions with cationic polymers. For such polymerization strategy, a major breakthrough is still needed to fully eliminate chemical processes and further improve the nanocomplex-forming ability of polymerized siRNAs. Herein, the extremely strong interaction between the DNA product of rolling circle amplification (RCA) and linear poly(ether imide) (PEI) has been disclosed; accordingly, a stable nanocomplex is formed just at its charge neutralization point, which benefits from the high molecular weight of the RCA product (>3 000 000 Da).

Fabrication and Biomedical Applications of "Polymer-Like" Nucleic Acids Enzymatically Produced by Rolling Circle Amplification.

Rolling circle amplification (RCA) is an isothermal enzymatic amplification reaction, which is used to massively produce periodic long-single-stranded DNA/RNA with predesigned sequences and functions. The RCA technique not only shows unparalleled advantages in constructing functional DNA assemblies; and the RCA products can also serve as high-performance scaffolds to interact with or accommodate foreign moieties, i.e.

Well-Optimized Conjugated GO-DNA Nanosystem for Sensitive Ratiometric pH Detection in Live Cells.

Intracellular pH is a vital parameter which can reflect the physiological process, and the detection of intracellular pH with a high signal-to-noise ratio (SNR) remains a challenge. Compared to pH biosensors based on a single-wavelength signal, it is much easier to obtain better sensitivity and higher SNR from the biosensors by two-wavelength ratiometric signals. In this study, we used DNA-grafted graphene oxide (GO) to ratiometrically detect intracellular pH ranging from basic to acidic.

CDPath: Cooperative Driver Pathways Discovery Using Integer Linear Programming and Markov Clustering.

Discovering driver pathways is an essential task to understand the pathogenesis of cancer and to design precise treatments for cancer patients. Increasing evidences have been indicating that multiple pathways often function cooperatively in carcinogenesis. In this study, we propose an approach called CDPath to discover cooperative driver pathways.