Article
Biology
Mark C. Johnson, Geylani Can, Miguel Monteiro Santos, Diana Alexander, Philip Zegerman
Summary: This study reveals that Rad53 phosphorylates the same substrates throughout the cell cycle, not just in S-phase, suggesting its roles beyond S-phase. By inhibiting 51d3 and Dbf4, Rad53 limits re-replication in G2/M, preventing gene amplification, and inhibiting these substrates in G1 prevents premature initiation at the G1/S transition. This redefinition of the 'S-phase checkpoint' has implications for understanding checkpoint function in cancers without proper cell cycle controls.
Article
Engineering, Chemical
Beatriz B. Cardoso, Jean-Michel Fernandes, Ana C. Pinheiro, Adelaide Braga, Sara C. Silverio, Ligia R. Rodrigues
Summary: The aim of this study was to establish a food-grade purification strategy for the production and purification of Epilactose, a functional sugar. Epilactose was produced by enzymatic epimerization and unreacted lactose was removed using a suitable 8-galactosidase enzyme. Monosaccharides generated during the reaction were eliminated through microbial treatment or activated charcoal. The resulting two-step process achieved an 87% purity and 76.4% yield of Epilactose. Additionally, the resistance of Epilactose to gastrointestinal conditions was evaluated using in vitro simulation, demonstrating its potential as a prebiotic.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Ishita Joshi, Jie Peng, Gina Alvino, Elizabeth Kwan, Wenyi Feng
Summary: This study compared replication origin activation in two yeast strains under hydroxyurea treatment, revealing the roles of S-phase checkpoint control, DNA sequence polymorphisms, and origin-transcription unit positioning. Rad53 protein plays a significant role in activation of origins, particularly in checkpoint-proficient cells.
Article
Computer Science, Hardware & Architecture
Yosef Masoudi-Sobhanzadeh, Shabnam Emami-Moghaddam
Summary: This study proposes a machine learning-based method to predict botnets, addressing the limitations of existing methods in real-time application, functionality, and consideration of attack types. The results show that the proposed method accurately classifies data streams into relevant groups and achieves a trade-off between feature selection and prediction model performance.
Article
Biochemistry & Molecular Biology
Fiona Jenkinson, Kang Wei Tan, Barbara Schopf, Miguel M. Santos, Philip Zegerman
Summary: In eukaryotes, cyclin-dependent kinase (CDK) inhibits helicase loading factors to ensure the exact duplication of the genome. CDK activates origin firing by phosphorylating Sld2 and Sld3, forming a transient intermediate called the pre-initiation complex (pre-IC). In yeast, the CDK phosphorylations of Sld3 and Sld2 are rapidly turned over by the phosphatases PP2A and PP4 during S phase. This dephosphorylation is important for genome-wide origin firing, pre-IC formation, and maintaining Sld3 dephosphorylation in G1 phase. PP2ARts1 specifically targets Sld3 and its dephosphorylation is critical for replication and cell viability.
Article
Biochemistry & Molecular Biology
Alex J. Whale, Michelle King, Ryan M. Hull, Felix Krueger, Jonathan Houseley
Summary: Adaptive mutations can cause drug resistance and increase tolerance to chemical treatment. The study investigates the transcription mechanism of the copper resistance gene CUP1 in budding yeast and its impact on copy number variation. The results demonstrate that CUP1 transcription requires TREX-2 and Mediator, and that replication stress and homologous recombination contribute to the amplification of CUP1 gene. The study also highlights the critical role of late-firing replication origins in CUP1 amplification.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biotechnology & Applied Microbiology
R. Sahaya Glingston, Jyoti Yadav, Jitika Rajpoot, Neha Joshi, Shirisha Nagotu
Summary: Yeast has been proven to be a valuable model system for studying viral infection and expression of viral proteins, advancing our understanding of important viruses. Through high-throughput analysis, genetic manipulation, and its compact genome, yeast provides insights into various aspects related to virus replication.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Philip S. Robinson, Tim H. H. Coorens, Claire Palles, Emily Mitchell, Federico Abascal, Sigurgeir Olafsson, Bernard Lee, Andrew R. J. Lawson, Henry Lee-Six, Luiza Moore, Mathijs A. Sanders, James Hewinson, Lynn Martin, Claudia M. A. Pinna, Sara Galvotti, Raheleh Rahbari, Peter J. Campbell, Inigo Martincorena, Ian Tomlinson, Michael R. Stratton
Summary: Research suggests that individuals with germline POLE or POLD1 mutations have increased mutational burdens in their somatic cells, yet do not exhibit overt signs of premature aging, besides a heightened risk of cancer. This indicates that normal cells are capable of tolerating high mutation rates.
Article
Multidisciplinary Sciences
Audra L. Amasino, Shalini Gupta, Larry J. Friedman, Jeff Gelles, Stephen P. Bell
Summary: Eukaryotic DNA replication occurs only once per cell cycle, which is regulated by the temporal separation of helicase loading and activation. Phosphorylation of ORC by CDK inactivates helicase loading by preventing the recruitment of a second Mcm2-7 helicase and destabilizing the first Mcm2-7 ring closure. This phosphorylation also inhibits the formation of the MO complex, which is necessary for stable closure of the first Mcm2-7. These findings demonstrate that ORC phosphorylation affects multiple steps of helicase loading and elucidate the two-step process of the first Mcm2-7 ring closure.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Minchao Jiang, Renfeng Zhang, Yixiao Xia, Gangyong Jia, Yuyu Yin, Pu Wang, Jian Wu, Ruiquan Ge
Summary: This article introduces a computational method called i2APP that can efficiently predict antiparasitic peptides. By extracting multi-level features and using machine learning algorithms for classification, this method achieves higher accuracy and AUC than existing methods on independent datasets.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Po-Hsuen Lee, Mary Ann Osley
Summary: A study revealed that quiescent cells undergo regulated DNA replication when resuming growth, with low levels of replication initiation factors requiring resynthesis, delaying entry into S phase. Fewer replication origins were activated in quiescent cells, with differences in chromatin structure compared to G1 cells.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Valentina Brancato, Nadia Brancati, Giusy Esposito, Massimo La Rosa, Carlo Cavaliere, Ciro Allara, Valeria Romeo, Giuseppe De Pietro, Marco Salvatore, Marco Aiello, Mara Sangiovanni
Summary: Breast cancer is the most common cancer among women worldwide, and its heterogeneity can be predicted through radiomics using medical imaging. However, the lack of comprehensive datasets and a general methodology limits the routine use of radiomics in breast cancer clinical practice.
Article
Food Science & Technology
Dianhui Wu, Ye Wu, Zixuan Gu, Xingguang Chen, Hua Liu, Jian Lu, Guangfa Xie
Summary: In this study, a S. cerevisiae strain NM-8 isolated from lemon was used for lemon wine fermentation. The results showed that NM-8 strain displayed good acidity tolerance and produced lemon wine with higher beneficial compounds and sensory score.
Article
Water Resources
Mohaddeseh Zahmatkesh Anbarani, Afsaneh Esmaeili Nasrabadi, Ziaeddin Bonyadi
Summary: The aim of this study was to evaluate the efficiency of S. cerevisiae in removing PS from aqueous solutions. BBD was used to determine the optimal removal conditions. The maximum PS removal efficiency was 98.81% under optimized conditions. Based on the results, it can be concluded that S. cerevisiae can be used as a natural and environmentally friendly biocoagulant to remove PS.
APPLIED WATER SCIENCE
(2023)
Article
Engineering, Biomedical
N. Jagan Mohan, R. Murugan, Tripti Goel, Seyedali Mirjalili, Parthapratim Roy
Summary: Diabetic retinopathy is a common complication of diabetes, with early detection crucial for preventing vision loss. The proposed ensemble deep neural network and feature selection technique achieved an accuracy of over 98% using a support vector machine classifier.
PHYSICAL AND ENGINEERING SCIENCES IN MEDICINE
(2021)
Article
Genetics & Heredity
Xianhai Li, Liu Xiang, Yue Lin, Qiang Tang, Fanbo Meng, Wei Chen
Summary: This study aims to explore the mechanism of Qingfei Paidu Decoction (QFPDD) in blocking the transition of COVID-19 patients from mild to severe stage. Through screening key ingredients and performing KEGG enrichment analysis, it was discovered that QFPDD can prevent the deterioration of COVID-19 by inhibiting relevant genes and multiple signaling pathways.
CURRENT GENE THERAPY
(2022)
Article
Biochemical Research Methods
Lirong Zhang, Yanchao Yang, Lu Chai, Qianzhong Li, Junjie Liu, Hao Lin, Li Liu
Summary: This study quantitatively analyzed the correlation between transcription factors (TFs) and gene expression and identified TF modules associated with gene expression. A convolutional neural network model, TFCNN, was constructed to predict gene expression levels based on the enrichment characteristics of TFs. Results showed that TFCNN achieved high prediction performance and outperformed other models by better extracting combinatorial interactions among TFs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Hao Lv, Yang Zhang, Jia-Shu Wang, Shi-Shi Yuan, Zi-Jie Sun, Fu-Ying Dao, Zheng-Xing Guan, Hao Lin, Ke-Jun Deng
Summary: In this study, a comprehensive method called iRice-MS based on eXtreme Gradient Boosting (XGBoost) was developed to identify multiple post-translational modifications (PTMs) in rice. The method displayed excellent performance in cross-validation and independent dataset test, and showed superiority to existing tools in terms of AUC value.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Hasan Zulfiqar, Qin-Lai Huang, Hao Lv, Zi-Jie Sun, Fu-Ying Dao, Hao Lin
Summary: The study aimed to establish a robust deep learning model to recognize 4mC sites in Geobacter pickeringii. By using different feature descriptors and optimization algorithms, the accuracy of the model was improved.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Meng Wu, Fulei Nie, Haibin Liu, Tianyang Zhang, Miaomiao Li, Xiaoming Song, Wei Chen
Summary: This study investigated 1592 m(6)A modification regulators from 65 representative plant species and analyzed their phylogenetic relationships, sequence structure, selection pressure, and codon usage. The study found that regulators from different species or subfamilies were distinguishable based on phylogenetic trees. The gene structure of regulators was conserved, but unique exon/intron structures and motif organizations were observed among different families. The analysis also demonstrated that regulators experienced purifying selection, and the selection pressure was more relaxed in higher plants, suggesting they might have acquired new functions during evolution. Additionally, different codon usage preferences were observed for different kinds of regulators.
Article
Biochemistry & Molecular Biology
Juanjuan Kang, Qiang Tang, Jun He, Le Li, Nianling Yang, Shuiyan Yu, Mengyao Wang, Yuchen Zhang, Jiahao Lin, Tianyu Cui, Yongfei Hu, Puwen Tan, Jun Cheng, Hailong Zheng, Dong Wang, Xi Su, Wei Chen, Yan Huang
Summary: The study updated the RNAInter database to version 4.0, which includes an enlarged data set and an updated confidence scoring system, providing a faster and more user-friendly interface, with over 47 million total entries. This will offer a more comprehensive and readily accessible RNA interactome platform for investigating the regulatory landscape of cellular RNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemical Research Methods
Li Liu, Kaiyuan Han, Huimin Sun, Lu Han, Dong Gao, Qilemuge Xi, Lirong Zhang, Hao Lin
Summary: This review provides an overview of loop-calling tools for various 3C-based techniques. It categorizes and summarizes these tools, discusses background biases and denoising algorithms, and helps researchers select the most appropriate method for loop calling and downstream analysis. It is also useful for bioinformatics scientists aiming to develop new loop-calling algorithms.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Xiang Feng, Hongqi Zhang, Hao Lin, Haixia Long
Summary: In this study, a directed graph neural network called scDGAE was developed for scRNA-seq analysis, using graph autoencoders and graph attention network. The experiment results showed that the scDGAE model achieved promising performance in gene imputation and cell clustering prediction, and it can be applied to general scRNA-Seq analyses.
Review
Medicine, Research & Experimental
Wei Chen, Xuesong Liu, Sanyin Zhang, Shilin Chen
Summary: Traditional wet laboratory testing and validations are costly and time-consuming for drug discovery. However, advancements in artificial intelligence (AI) techniques are changing the landscape of drug discovery. Combined with accessible data resources, AI techniques have accelerated the drug discovery process and have been widely applied in pharmaceutical analysis and drug design. Nonetheless, there are challenges in applying AI to drug discovery.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Chemistry, Medicinal
Xiao-Wei Liu, Tian-Yu Shi, Dong Gao, Cai-Yi Ma, Hao Lin, Dan Yan, Ke-Jun Deng
Summary: Diabetes mellitus is a chronic metabolic disease that disrupts blood glucose homeostasis and leads to severe complications. The development of artificial intelligence has provided a powerful tool, iPADD, for accelerating the discovery of potential antidiabetic drugs. iPADD achieved high accuracy in drug prediction by using molecular fingerprints and machine learning algorithms.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Medicine, General & Internal
Wen Zhu, Shi-Shi Yuan, Jian Li, Cheng-Bing Huang, Hao Lin, Bo Liao
Summary: This study provides the first recognition framework for accurately identifying HBP based on machine learning. By using four sequence descriptors, HBP and non-HBP samples were represented by discrete numbers and input into SVM and RF algorithms for comparison. The SVM-based classifier was found to have the greatest potential for identifying HBP.
Review
Biochemistry & Molecular Biology
Hasan Zulfiqar, Zhiling Guo, Bakanina Kissanga Grace-Mercure, Zhao-Yue Zhang, Hui Gao, Hao Lin, Yun Wu
Summary: Hormone binding proteins (HBPs) belong to soluble carrier proteins that interact selectively and non-covalently with hormones, promoting growth hormone signaling in humans and other animals. The identification of HBPs is crucial for understanding these proteins and their applications in medical and commercial fields. Computational prediction methods, using sequence information and machine learning algorithms, have played a significant role in recognizing HBPs, offering a time-saving and cost-effective alternative to experimental methods.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Medicine, Research & Experimental
Kexing Xi, Mengqing Zhang, Mingrui Li, Qiang Tang, Qi Zhao, Wei Chen
Summary: In this study, a network-based methodology was used to explore the mechanisms of nephrotoxicity induced by specific compounds. The results showed that the advanced glycosylation end products-receptor for advanced glycosylation end products signaling pathway, human cytomegalovirus infection, lipid and atheroapoptosis, and the phosphatidylinositol 3-kinase-Akt pathways play important roles in nephrotoxicity.
MOLECULAR THERAPY NUCLEIC ACIDS
(2023)
Article
Biodiversity Conservation
Wenfei Liao, Hao Lin
Summary: Urbanisation has complex effects on the morphological traits of aquatic insect species, with different species exhibiting different strategies and abilities to cope with movement barriers caused by urbanisation.
INSECT CONSERVATION AND DIVERSITY
(2023)
Article
Biology
Jie Gao, Yongxian Feng, Yan Yang, Yuetong Shi, Junjie Liu, Hao Lin, Lirong Zhang
Summary: This study systematically identified and analyzed key CpG sites closely related to differential expression of genes in LUSC through a two-step correlation analysis method, and found that these sites and genes can serve as effective biomarkers for LUSC.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
