Article
Chemistry, Multidisciplinary
Mohibullah Shah, Samavia Jaan, Muhammad Shehroz, Asifa Sarfraz, Khamna Asad, Tehreem Ul Wara, Aqal Zaman, Riaz Ullah, Essam A. Ali, Umar Nishan, Suvash Chandra Ojha
Summary: This study presents a reverse vaccinology approach using a messenger RNA (mRNA) vaccine to target the Monkeypox virus (MPXV). Through bioinformatic tools, potential B and T lymphocyte epitopes were predicted and antigenic proteins were identified. The mRNA vaccine was found to have a stable structure and efficient expression in host cells, with strong interactions observed with toll-like receptors 2 (TLR2) and 4 (TLR4). In silico immune simulation analyses demonstrated enhanced immune responses following repeated exposure to the designed vaccine. Overall, the vaccine candidate designed in this study holds promise as a novel mRNA therapeutic vaccine against MPXV infection.
Article
Biochemistry & Molecular Biology
Adrian Lopez Martin, Mohamed Mounir, Irmtraud M. Meyer
Summary: RNA structure formation in vivo occurs co-transcriptionally, involving transient RNA structure features that are not part of the final functional structure. COBOLD is a computational method for identifying different classes of transient RNA structure features that can aid or hinder the formation of a known reference RNA structure. It is available as a web-server with dedicated data visualization.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Xiaojing Cong, Wenwen Ren, Jody Pacalon, Rui Xu, Lun Xu, Xuewen Li, Claire A. de March, Hiroaki Matsunami, Hongmeng Yu, Yiqun Yu, Jerome Golebiowski
Summary: This study investigated how the amino-acid sequences of olfactory receptors (ORs) encode diversified responses to various ligands. Using a proteochemometric model, the researchers were able to predict OR responses to odorants and discover new OR-ligand pairs. This approach will contribute to the mapping of OR-odorant interactions and the identification of orphan receptors.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemical Research Methods
Wei He, Helen Wang, Yanjun Wei, Zhiyun Jiang, Yitao Tang, Yiwen Chen, Han Xu
Summary: This study developed an integrative prediction method GuidePro that prioritizes sgRNAs in protein knockouts by incorporating multiple factors. Tested on independent datasets, GuidePro demonstrated superior performance in predicting phenotypes caused by protein loss-of-function, suggesting its robustness in various applications of CRISPR/Cas9 knockouts.
Article
Biochemistry & Molecular Biology
Gerard Minuesa, Cristina Alsina, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Ivan Dotu
Summary: MoiRNAiFold is a versatile and user-friendly tool for de novo synthetic RNA design, based on Constraint Programming, with the ability to handle multiple design constraints and quality measures, and improve features for RNA regulation control of gene expression. Demonstrated to outperform any previous software in benchmarking structural RNA puzzles from EteRNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar
Summary: Access pathways are critical for substrate and product transport in enzymes. A Python3 API called pyCaverDock is introduced to enhance the user experience and facilitate ligand transport analysis. This API simplifies the steps needed to use CaverDock and allows for automation of setup processes.
Article
Biochemistry & Molecular Biology
Alexander R. van Vliet, George N. Chiduza, Sarah L. Maslen, Valerie E. Pye, Dhira Joshi, Stefano De Tito, Harold B. J. Jefferies, Evangelos Christodoulou, Chloe Roustan, Emma Punch, Javier H. Hervas, Nicola O'Reilly, J. Mark Skehel, Peter Cherepanov, Sharon A. Tooze
Summary: ATG9A and ATG2A are essential core members of the autophagy machinery. Researchers have identified the molecular details of their interaction and demonstrated their importance for autophagy using structural modeling and functional activity analysis.
Article
Multidisciplinary Sciences
Fatemeh Sabzian-Molaei, Mohammad Ali Nasiri Khalili, Mohammad Sabzian-Molaei, Hosein Shahsavarani, Alireza Fattah Pour, Ahmad Molaei Rad, Amin Hadi
Summary: This study investigates the interaction between Urtica dioica agglutinin (UDA) and the spike protein receptor-binding domain (RBD) of SARS-CoV-2. The results show that UDA can bind to the RBD and inhibit the attachment of the virus to ACE2 receptor on the host cell. The findings suggest that UDA has the potential to be developed as an effective inhibitor against SARS-CoV-2 infection.
Article
Multidisciplinary Sciences
Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M. Bourdakou, Pavlos Pavlidis, George M. Spyrou
Summary: This study utilizes global genetic data and public health information to select informative SARS-COV-2 mutations in a more precise way, deepening our understanding of the relationship between viral mutations and virulence, and providing important insights for future virus research.
Article
Biochemistry & Molecular Biology
Joshua S. Martin Beem, Sravani Venkatayogi, Barton F. Haynes, Kevin Wiehe
Summary: Antibodies are generated by B cells through rounds of mutation and selection, and a program called ARMADiLLO has been developed to estimate the probabilities of observed antibody mutations. The ARMADiLLO web server provides an easy-to-use interface for analyzing antibody sequences and displaying the probability estimates for all possible amino acid changes. The probabilities of antibody mutations can be used by immunologists studying B cell ontogenies and vaccine designers pursuing strategies to elicit broadly neutralizing antibodies enriched with unlikely mutations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Dominik Kopczynski, Nils Hoffmann, Nina Troppmair, Cristina Coman, Kim Ekroos, Michael R. Kreutz, Gerhard Liebisch, Dominik Schwudke, Robert Ahrends
Summary: Lipid analysis is important for understanding the various functions of lipids, and LipidSpace is a standalone tool that analyzes lipidomes by assessing their structural and quantitative differences. It offers a user-friendly GUI and support for multiple data formats, allowing for reanalysis and merging of datasets, and provides additional discoveries.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Diego de S. Lima, Luiz J. A. Amichi, Maria A. Fernandez, Ademir A. Constantino, Flavio A. V. Seixas
Summary: In this study, an attention-based LSTM network was developed and a classification model was built to directly classify short non-coding RNAs (including Y RNA) from nucleotide sequences. The performance evaluation demonstrated that the proposed method accurately predicts Y RNA sequences and their homologs, as well as 11 additional classes, achieving comparable results with state-of-the-art methods. Furthermore, applying t-SNE on learned sequence representations was shown to be useful for sequence analysis.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Minh N. Nguyen, Nora L. Krutz, Vachiranee Limviphuvadh, Andreas L. Lopata, G. Frank Gerberick, Sebastian Maurer-Stroh
Summary: AllerCatPro 2.0 is a web server for predicting the allergenic potential of proteins with better accuracy than other methods, and new features to help assessors make informed decisions. It predicts protein similarity using amino acid sequences and predicted 3D structures.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ahmed Mohamed, Dharmesh D. Bhuva, Sam Lee, Ning Liu, Chin Wee Tan, Melissa J. Davis
Summary: vissE.Cloud is a webserver for gene-set analysis, offering summarisation and interactive visualisation of GSA results. It allows analysis of gene lists as well as raw single-cell and spatial omics data, making it the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Qiaoqiao Huang, Ying Han, Edward Shen, Ziyang Feng, Yinghui Peng, Le Gao, Yan Gao, Yongtin Yu, Wei Li, Ping Liu, Cao Guo, Shan Zeng, Changjing Cai, Hong Shen
Summary: MTFR2 is upregulated in hepatocellular carcinoma (HCC) and is associated with immune cell infiltration and immunotherapy. It plays a significant role in poor prognosis of HCC.
Article
Operations Research & Management Science
Wei Lu, Yu Jiang, Panpan Xia, Zhimin Huang
Summary: This study examines how retailer overconfidence affects the supply chain transparency for manufacturers. The results show that in the reselling model, overconfident retailers have a stronger incentive to increase supply chain transparency compared to the agency selling model. Surprisingly, even at a moderate channel substitution rate, overconfident retailers may still promote supply chain transparency, contrary to conventional wisdom. Additionally, from the perspective of entry cost, overconfident retailers are more motivated to increase transparency in the reselling model compared to normal retailers. For the agency selling model, these findings are reversed. Overall, the study sheds light on why some retailers voluntarily share information with manufacturers and highlights the potential benefits of overconfidence bias in certain situations.
ANNALS OF OPERATIONS RESEARCH
(2023)
Article
Biochemical Research Methods
Xiaokun Hong, Ningshan Li, Jiyang Lv, Yan Zhang, Jing Li, Jian Zhang, Hai-Feng Chen
Summary: In this study, a publicly accessible PTMint database was constructed, which contains complete experimental evidence of PTM regulation on PPIs in multiple organisms, covering various diseases. The establishment of this database helps in gaining insight into disease mechanisms, disease diagnosis, and drug discovery associated with PTM and PPI.
Article
Energy & Fuels
Wenbin Cai, Huiren Zhang, Zhimin Huang, Xiangyang Mo, Kang Zhang, Shun Liu
Summary: The Sulige Gas Field, a low-permeability tight gas sandstone field, has experienced a decline in natural gas production due to liquid accumulation in the wellbore caused by below-critical flow rates of the wells. Plunger lift technology, known for its simple installation and operation, low cost, and high liquid-carrying capacity, has proven to be effective in removing liquids from the wells in the Sulige Gas Field.
Article
Engineering, Chemical
Zhimin Huang, Wenbin Cai, Huiren Zhang, Xiangyang Mo
Summary: The Changbei gas field experiences severe liquid loading in gas wells, leading to a rapid decrease in production. A method was established to identify the water source and evaluate the condensate content in the gas well. Additionally, a method was developed to distinguish the start time of liquid loading and estimate its depth based on bottomhole pressure. This study provides insights into liquid loading in gas wells and lays a foundation for the development of deliquification techniques.
Article
Geosciences, Multidisciplinary
Wenbin Cai, Xiangyang Mo, Wen Li, Shun Liu, Desheng Zhou, Huiren Zhang, Zhimin Huang
Summary: This study analyzed the onsite fatigue damage and stress distribution in pumping rods in depth. Macroscopic morphology and chemical properties of fatigue damage were analyzed. The crystalline phase composition and hardness of fatigue damage were analyzed. Stress distribution was analyzed in terms of rod-body stress and connection-section stress. The study also summarized the cross-sectional characteristics of fatigue crack expansion and identified the types of fatigue fracture and influencing factors of the pumping rod. Modeling and stress analysis of the pumping rod were performed using SolidWorks and ABAQUS software. By comparing stress cloud diagrams of different thread root shapes, the factors causing fracture in the pumping rod and the locations of stress concentrations and dangerous cross-sections were determined.
FRONTIERS IN EARTH SCIENCE
(2023)
Article
Chemistry, Medicinal
Xiaoyue Ji, Xiaochen Cui, Zhengxin Li, Taeyoung Choi, Ying Wang, Wen Xiao, Yunshuo Zhao, Jinyin Zha, Jian Zhang, Hai-Feng Chen, Zhengtian Yu
Summary: Allosteric modulators are regulatory elements that bind to allosteric sites and can impact the properties of proteins. Molecular dynamics simulation has become an important complement to experimental methods in identifying allosteric sites. In this study, a precise force field called APSF was developed using deep learning and reweighting methods, and its performance was evaluated on multiple allosteric proteins. The results showed that APSF could effectively capture different types of allosteric pockets and sample multiple energy-minimum reference conformations. The efficiency of conformation sampling for APSF was also higher than the current force field ff14SB. These findings highlight the potential of APSF in identifying allosteric sites and screening allosteric drugs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Environmental Sciences
Kai Xin, Ruhan Guo, Xiangbo Zou, Mumin Rao, Zhimin Huang, Cao Kuang, Ji Ye, Chuangting Chen, Cong Huang, Maoqiang Zhang, Weijuan Yang, Jun Cheng
Summary: To improve the CO2 biofixation efficiency of microalgae cultivated with coal-chemical flue gas, CO2 gradient domestication was used to enhance high-concentration CO2 tolerance and photoautotrophic growth of acid-tolerant Euglena gracilis. The results showed that CO2 gradient domestication significantly increased the biomass yield, RuBisCO activity, and chlorophyll content of E. gracilis. Moreover, the domesticated strain exhibited higher antioxidant enzyme activities and lower apoptotic and necrotic rates under high carbon stress. This study provides valuable guidance for CO2 fixation and adaptive evolution of E. gracilis in industrial flue gas.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Respiratory System
Liping Huang, Shuyun Xu, Zhimin Huang, Yusheng Chen, Nengluan Xu, Baosong Xie
Summary: The accurate prediction of the development of Pneumocystis jirovecii pneumonia (PJP) in non-HIV immunocompromised patients is still unclear. Concomitant use of corticosteroids and immunosuppressant and lymphocyte counts < 0.7 x 10(9)/L are risk factors for the development of PJP in non-HIV immunocompromised patients. Metagenomic next-generation sequencing (mNGS) reveals that mixed infections, including CMV, EBV, and Candida, are common in PJP patients.
BMC PULMONARY MEDICINE
(2023)
Article
Nutrition & Dietetics
Suyan Duan, Si Chen, Fang Lu, Meng Zhou, Ling Jiang, Chen Chen, Luhan Geng, Rui Sun, Yili Xu, Zhimin Huang, Chengning Zhang, Bo Zhang, Huijuan Mao, Changying Xing, Yanggang Yuan
Summary: This study aims to clarify the association between 25(OH)D levels and disease severity and therapy response of primary membranous nephropathy (PMN). The results showed that baseline 25(OH)D levels were correlated with manifestations of nephrotic syndrome and seropositivity of anti-PLA2R Ab in PMN patients. In the follow-up cohort, a low level of 25(OH)D was demonstrated as an independent risk factor for non-remission. Therefore, 25(OH)D levels may serve as a prognostic tool to sensitively identify patients with a high probability of poor treatment response.
FRONTIERS IN NUTRITION
(2023)
Article
Energy & Fuels
Chengdong Ying, Qinhui Wang, Yunjin Yang, Zhimin Huang, Yao Zhu, Jianmeng Cen
Summary: In this study, the effects of temperature, CaO absorbent, and atmosphere on sulfur transformation in coal steam gasification were investigated. It was found that an increase in temperature enhanced the formation of organic sulfur while reducing the amount of sulfur in the absorbent. CaO promoted sulfur conversion and acted as a sulfur absorbent and removal agent. The presence of CaO also decreased the release of H2S. In addition, the sulfur conversion was influenced by the atmosphere, with steam atmosphere leading to higher H2S-S but lower absorbent-S compared to inert atmosphere.
Article
Biochemistry & Molecular Biology
Jixiao He, Xinyi Liu, Chunhao Zhu, Jinyin Zha, Qian Li, Mingzhu Zhao, Jiacheng Wei, Mingyu Li, Chengwei Wu, Junyuan Wang, Yonglai Jiao, Shaobo Ning, Jiamin Zhou, Yue Hong, Yonghui Liu, Hongxi He, Mingyang Zhang, Feiying Chen, Yanxiu Li, Xinheng He, Jing Wu, Shaoyong Lu, Kun Song, Xuefeng Lu, Jian Zhang
Summary: This article introduces the role and importance of allosteric regulation in fine-tuning macromolecular function. It also highlights the recent updates in the Allosteric Database (ASD), including potential allosteric sites, allosteric protein-protein interaction modulators, and allosteric hit-to-lead compounds. These novel features make ASD a comprehensive database, facilitating allosteric target identification, mechanistic exploration, and drug discovery.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Environmental Sciences
Lingchong Feng, Zhenyi Wang, Dongwei Jia, Xiangbo Zou, Mumin Rao, Zhimin Huang, Cao Kuang, Ji Ye, Chuangting Chen, Cong Huang, Maoqiang Zhang, Jun Cheng
Summary: This study aimed to determine the optimal CO2 concentration for microalgal biomass production with industrial flue gas. By analyzing the metabolism pathways of Nannochloropsis oceanica (N. oceanica) under different nitrogen/phosphorus (N/P) nutrients and CO2 concentrations, the researchers found that the optimum CO2 concentration was 70% under 100% N/P nutrients, and 50% for N or P deficiency and 30% for both N and P deficiency. The optimal combination of CO2 concentration and N/P nutrients enhanced photosynthetic electron transfer efficiency and carbon metabolism, but inappropriate combinations led to errors in DNA replication and protein synthesis, inhibiting carbon fixation and biomass production.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Chemistry, Multidisciplinary
Zhongmin Wang, Jing Qu, Yanxiang He, Tuzhi Xiong, Zhimin Huang, Feng Wang, M. -Sadeeq Balogun
Summary: This study successfully synthesized a Mo-based nitride/oxide electrocatalyst Ni0.2Mo0.8N/MoO2, which exhibits impressive catalytic performance towards alkaline hydrogen evolution (HER). The optimized catalyst shows an ultralow overpotential of 13 mV at a current density of 10 mA cm(-2), outperforming the corresponding oxide counterpart (NiMoO4/MoO2, 162 mV) and benchmark Pt/C catalyst (27 mV). The experimental results reveal that MoO2 enhances the H2O dissociation kinetics, while Ni0.2Mo0.8N exhibits favorable H adsorption energy, leading to accelerated HER kinetics of the Ni0.2Mo0.8N/MoO2 catalyst. This work provides important insights for the rational design of highly efficient HER electrocatalysts.
MATERIALS CHEMISTRY FRONTIERS
(2023)
Article
Chemistry, Organic
Fengkai Sun, Man Miao, Wenxue Li, Xiao-Bing Lan, Jian-Qiang Yu, Jian Zhang, Zhenyu An
Summary: An array of pyrrolo[1,2-a]quinoxaline derivatives were synthesized with moderate to good yields via the electrochemical redox reaction, involving the functionalization of C(sp(3))-H bonds and construction of C-C and C-N bonds. This atom economical reaction utilized THF as both a reactant and a solvent, with H-2 as the sole by-product.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Jinyin Zha, Jixiao He, Chengwei Wu, Mingyang Zhang, Xinyi Liu, Jian Zhang
Summary: Traditionally, drugs have targeted only one site on the protein surface, which limits their potency and selectivity. Dualsteric modulators, with their bivalent nature, offer a solution by targeting both orthosteric and allosteric sites, allowing for a balance of potency and selectivity, and overcoming drug resistance. They can also be used for designing fluorescent tracers and studying protein conformations.
CHEMICAL SOCIETY REVIEWS
(2023)
