Publications by authors named "Yaoqi Zhou"

Article Synopsis
  • Efficient electrocatalysts, especially medium-entropy oxides (MEOs), are essential for improving the hydrogen evolution reaction (HER) due to their unique properties like multiple components and lattice distortion.
  • This study utilizes soluble soybean polysaccharide (SSPS) as a template to create an FeCoNiO/C composite, which enhances the formation of important features such as oxygen vacancies and a favorable nanoparticle shape.
  • The resulting O vacancy-modified FeCoNiO/C composite shows excellent HER performance, requiring only 61 mV overpotential for achieving a 10 mA cm current density, indicating its potential as an effective electrocatalyst for industrial use.
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X-ray crystallography is a fundamental technique that provides atomic-level insights into RNA structures. However, obtaining crystals of RNA structures diffracting to high resolution is challenging. We introduce a simple strategy to enhance the resolution limit of RNA crystals by the selective substitution of Watson-Crick pairs by GU pairs within RNA sequences.

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  • The study highlights the rarity and under-exploration of self-cleaving ribozymes in the human genome, focusing on LINE-1 and OR4K15.
  • Researchers found that these ribozymes consist of two short essential segments totaling only 35 and 31 nucleotides, making them the simplest known self-cleaving ribozymes.
  • The ribozymes exhibit unique structural characteristics, resembling lantern shapes, with significant differences in mutational impact compared to related ribozyme classes, suggesting they represent a primitive ribozyme structure.
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RNA functions by interacting with its intended targets structurally. However, due to the dynamic nature of RNA molecules, RNA structures are difficult to determine experimentally or predict computationally. Artificial intelligence (AI) has revolutionized many biomedical fields and has been progressively utilized to deduce RNA structures, target binding, and associated functionality.

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The pore-throat structure is a crucial parameter for evaluating reservoir characteristics and assessing the potential of oil and gas resources. Understanding the relationship between reservoir pore-throat variations and oil-bearing properties is essential. Through a combination of techniques, including thin-section casting, scanning electron microscopy (SEM), micro-computed tomography (micro-CT), and high-pressure mercury injection (HPMI), we examined the tight sandstone reservoirs from the Chang 4 + 5 members of the Yanchang Formation in the study area.

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Recent success of AlphaFold2 in protein structure prediction relied heavily on co-evolutionary information derived from homologous protein sequences found in the huge, integrated database of protein sequences (Big Fantastic Database). In contrast, the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search. Here, we built a comprehensive database by incorporating the non-coding RNA (ncRNA) sequences from RNAcentral, the transcriptome assembly and metagenome assembly from metagenomics RAST (MG-RAST), the genomic sequences from Genome Warehouse (GWH), and the genomic sequences from MGnify, in addition to the nucleotide (nt) database and its subsets in National Center of Biotechnology Information (NCBI).

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Despite intensive search over the past decades, only a few small-molecule DNA fluorescent dyes were found with large Stokes shifts. These molecules, however, are often too toxic for widespread usage. Here, we designed DNA-specific fluorescent dyes rooted in benzimidazole architectures with a hitherto unexplored molecular framework based on thiazole-benzimidazole scaffolding.

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Article Synopsis
  • Recent advancements in deep learning have enhanced the inference of protein sequences from structures, with techniques evolving from basic neural networks to more complex models like GNNs.
  • The introduction of SPIN-CGNN utilizes protein contact maps for better nearest neighbor identification, improving the use of edge information in GNNs.
  • SPIN-CGNN demonstrated strong performance, matching AlphaFold2 in refolding ability while surpassing it in sequence recovery and other metrics, although low complexity regions still need refinement compared to native sequences.
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Long noncoding RNAs (lncRNAs) have emerged as crucial regulators across diverse biological processes and diseases. While high-throughput sequencing has enabled lncRNA discovery, functional characterization remains limited. The EVLncRNAs database is the first and exclusive repository for all experimentally validated functional lncRNAs from various species.

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Compared with proteins, DNA and RNA are more difficult languages to interpret because four-letter coded DNA/RNA sequences have less information content than 20-letter coded protein sequences. While BERT (Bidirectional Encoder Representations from Transformers)-like language models have been developed for RNA, they are ineffective at capturing the evolutionary information from homologous sequences because unlike proteins, RNA sequences are less conserved. Here, we have developed an unsupervised multiple sequence alignment-based RNA language model (RNA-MSM) by utilizing homologous sequences from an automatic pipeline, RNAcmap, as it can provide significantly more homologous sequences than manually annotated Rfam.

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We describe the modeling method for RNA tertiary structures employed by team AIchemy_RNA2 in the 15th Critical Assessment of Structure Prediction (CASP15). The method consists of the following steps. Firstly, secondary structure information was derived from various manually-verified sources.

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The outbreak of the novel coronavirus SARS-CoV-2 has posed a significant threat to human health and the global economy since the end of 2019. Unfortunately, due to the virus's rapid evolution, preventingand controlling the epidemic remains challenging. The ORF8 protein is a unique accessory protein in SARS-CoV-2 that plays a crucial role in immune regulation, but its molecular details are still largely unknown.

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Objective: Previous studies have indicated that neurotransmitters play important roles in the occurrence and development of gastric cancer. MAOA is an important catecholamine neurotransmitter-degrading enzyme involved in the degradation of norepinephrine, epinephrine and serotonin. To find a potential therapeutic target for the treatment of gastric cancer, the biological functions of MAOA and the underlying mechanism in gastric cancer need to be explored.

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Article Synopsis
  • Hyperactivation of ribosome biogenesis, particularly through the HEATR1 protein, is linked to the development and progression of hepatocellular carcinoma (HCC).
  • The study identified that HEATR1 is significantly overexpressed in HCC samples and correlates with poor patient survival and aggressive tumor characteristics.
  • Various molecular techniques were employed to validate the role of HEATR1 in HCC, including gene knockdown experiments, protein interaction analysis, and assessments of cellular growth and apoptosis.
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Determining intrinsically disordered regions of proteins is essential for elucidating protein biological functions and the mechanisms of their associated diseases. As the gap between the number of experimentally determined protein structures and the number of protein sequences continues to grow exponentially, there is a need for developing an accurate and computationally efficient disorder predictor. However, current single-sequence-based methods are of low accuracy, while evolutionary profile-based methods are computationally intensive.

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  • Gastric cancer is a serious disease that often spreads to the liver, making it harder to treat, and SLITRK4 is a protein that may play a key role in this process.
  • Researchers studied SLITRK4 to see how it affects gastric cancer and its spread to the liver, using various tests on cells and mice.
  • They found that higher levels of SLITRK4 are linked to worse outcomes for patients, and targeting SLITRK4 could be a possible new way to help treat gastric cancer that has spread to the liver.
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The extracellular matrix (ECM), as an important component of the tumor microenvironment, exerts various roles in tumor formation. Mitochondrial dynamic disorder is closely implicated in tumorigenesis, including hyperfission in HCC. We aimed to determine the influence of the ECM-related protein CCBE1 on mitochondrial dynamics in HCC.

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Ebola virus (EBOV) causes hemorrhagic fever in humans with high morbidity and fatality. Although over 45 years have passed since the first EBOV outbreak, small molecule drugs are not yet available. Ebola viral protein VP30 is a unique RNA synthesis cofactor, and the VP30/NP interaction plays a critical role in initiating the transcription and propagation of EBOV.

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SARS-CoV-2 has caused a global pandemic of COVID-19, posing a huge threat to public health. The SARS-CoV-2 papain-like cysteine protease (PLpro) plays a significant role in virus replication and host immune regulation, which is a promising antiviral drug target. Several potential inhibitors have been identified in vitro.

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Article Synopsis
  • Long non-coding RNAs (lncRNAs) are crucial in various biological processes and diseases, but only a small number have been experimentally validated, making computational tools necessary to prioritize potentially functional lncRNAs.
  • Researchers developed deep learning algorithms to differentiate verified lncRNAs from those that may not be functional, using three layers of neural networks tailored for human, mouse, and plant species.
  • The new models significantly outperformed previous methods, with the human model achieving an area under the curve score of 0.896, and the models are accessible online for use in screening lncRNA transcripts.
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The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means.

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Given the challenges for the experimental determination of RNA tertiary structures, probing solvent accessibility has become increasingly important to gain functional insights. Among various chemical probes developed, backbone-cleaving hydroxyl radical is the only one that can provide unbiased detection of all accessible nucleotides. However, the readouts have been based on reverse transcription (RT) stop at the cleaving sites, which are prone to false positives due to PCR amplification bias, early drop-off of reverse transcriptase, and the use of random primers in RT reaction.

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Article Synopsis
  • Connexins are special proteins that help cells communicate and can form groups of six to move things between them.
  • In a study on pancreatic cancer, researchers found that a protein called GJB3 was increased in cancer that had spread to the liver.
  • They discovered that lowering GJB3 stopped the cancer from spreading and that GJB3 helps recruit immune cells (neutrophils) to the tumors, so it could be a target for new treatments.
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  • Liver fibrosis, a process linked to chronic liver injury, results from excess extracellular matrix accumulation, primarily due to activated hepatic stellate cells (HSCs).
  • Disulfiram (DSF), a drug primarily used for alcohol addiction, shows potential anti-cancer effects and raises interest in its role against liver fibrosis and overall liver function.
  • In experiments with rat models, low-dose DSF was found to reduce liver fibrosis and improve liver function by significantly suppressing the activation and proliferation of HSCs, while promoting apoptosis in these cells.
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