Article
Computer Science, Information Systems
Shanchen Pang, Tong Ding, XiaoBing Mao, Neal N. Xiong
Summary: This study presents a new model of P system called conditional enzymatic numerical P system (DENPS), which introduces a series of decisional enzymes and rebuilds the cell structures to achieve a more flexible decision-making mechanism. The validation experiments demonstrate that DENPS is logical and efficient in processing large-scale decision tasks, with prior results being achieved 188.28 times faster and decision tree based on DENPS being 119.85 times faster than the general serial framework.
INFORMATION SCIENCES
(2021)
Article
Automation & Control Systems
Xiang Ren, Jorge Gomez, Mohammad Khairul Bashar, Jiaying Ji, Uryan Isik Can, Hsueh-Chia Chang, Nikhil Shukla, Suman Datta, Pinar Zorlutuna
Summary: Current designs for biocomputing are slow but efficient for information storage, while utilizing electrically active cells in networks can lead to faster parallel processing and solving computationally hard problems.
ADVANCED INTELLIGENT SYSTEMS
(2021)
Article
Cell Biology
Wei Wang, Yongqing Wang, Yu Zhang, Dong Liu, Hongjun Zhang, Xianfang Wang
Summary: In this study, a novel method called PPDTS was proposed to predict potential drug-target interactions by analyzing the local structure of drug-target association networks. The experimental performance of PPDTS outperformed four popular network-based similarity methods, as validated in different experimental datasets.
IET SYSTEMS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daniel Shoup, Andrew Roth, Jason Puchalla, Hays S. Rye
Summary: Protein aggregation can cause cellular dysfunction and disease and molecular chaperones are responsible for disassembling protein aggregates. Using Burst Analysis Spectroscopy, researchers found that the overall size of an aggregate has minimal influence on disassembly, while changes in internal structure can dramatically limit the ability to disassemble aggregates. These structural alterations progress quickly, making aggregates resistant to disassembly within minutes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Akiko Hatakeyama, Yuliia Shymko, Brigitte Hartmann, Romain Retureau, Claude Nogues, Marco Pasi, Malcolm Buckle
Summary: This study uses PhAST technology to investigate the structural changes of nucleosomes, revealing similarities and differences between nucleosome assembly and disassembly processes. The results suggest that the efficiency of DNA-histone binding is influenced by the DNA sequence and the amplitude of PhAST signals changes differently during assembly and disassembly. These findings provide new insights into the role of DNA sequence in gene expression regulation and shed light on how the intrinsic properties of DNA are integrated into the control of chromatin structure.
Article
Chemistry, Multidisciplinary
Jinlong Ma, Peng Wang, Huijia Li
Summary: Existing studies have mainly focused on the disassembly of undirected networks, with few studies on directed networks. To address this problem, an effective edge module disassembly method based on a non-backtracking matrix is proposed, which finds the minimum set of key points connecting different edge modules for removal to achieve the disassembly of directed networks.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Feng Wang, Xiang Feng, Qing He, Hua Li, Huilin Li
Summary: In this study, cryo-EM analysis revealed that the Saccharomyces cerevisiae Yta7 protein assembles into a three-tier hexamer structure, consisting of a top bromodomain (BRD) tier, a middle AAA1 tier, and a bottom AAA2 tier. The BRD of Yta7 stabilizes a four-stranded beta-helix structure called BRD-interacting motif (BIM) in the N-terminal region. Both the BRD and BIM contribute to nucleosome recognition and Yta7 binds to both acetylated and nonacetylated H3 peptides with higher affinity for the unmodified peptide. Overall, this study provides insights into the nucleosome disassembly process by Yta7.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Computer Science, Information Systems
Ben Niu, Bowen Xue, Huifen Zhong, Haiyun Qiu, Tianwei Zhou
Summary: This paper focuses on the aviation maintenance technician scheduling problem and proposes a practical dynamic task disassembly mechanism. By applying the mechanism, overtime work can be flexibly disassembled or reassigned based on work efficiency and progress, resulting in shorter maintenance time and lower total costs.
INFORMATION SCIENCES
(2023)
Article
Automation & Control Systems
Jin Xie, Xinyu Li, Liang Gao
Summary: Disassembly sequence planning (DSP) plays a crucial role in increasing efficiency, reducing costs, and minimizing environmental impacts. A modified grey wolf optimizer (MGWO) is proposed to address the NP-hard combinatorial optimization problem of DSP, introducing new operators to ensure feasibility of solutions and achieve effective results in engineering cases.
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY
(2021)
Article
Cell Biology
Micah J. McCauley, Michael Morse, Nicole Becker, Qi Hu, Maria Victoria Botuyan, Emily Navarrete, Ran Huo, Uma M. Muthurajan, Ioulia Rouzina, Karolin Luger, Georges Mer, James Maher, Mark C. Williams
Summary: The histone chaperone FACT enhances transcription by targeting DNA-protein interactions. This study demonstrates the impact of FACT on nucleosome stability and dynamics, revealing contradictory functions of different FACT subdomains in nucleosome remodeling. These findings provide insights into the catalytic role of key FACT domains in nucleosome disassembly and reassembly.
Review
Biotechnology & Applied Microbiology
Brett J. Kagan, Christopher Gyngell, Tamra Lysaght, Victor M. Cole, Tsutomu Sawai, Julian Savulescu
Summary: This article reviews the key aspects of Synthetic Biological Intelligence (SBI), its potential applications, and the associated ethical concerns. It aims to provide a robust framework for the responsible research and application of SBI technology.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Genetics & Heredity
Abdur Rasool, Qingshan Jiang, Yang Wang, Xiaoluo Huang, Qiang Qu, Junbiao Dai
Summary: This paper proposes a computational evolutionary approach based on a synergistic moth-flame optimizer to optimize DNA sequence encoding and decoding problems. The approach improves the efficiency and reduces errors of DNA storage by constructing reverse-complement constraints.
FRONTIERS IN GENETICS
(2023)
Article
Automation & Control Systems
Fei Wang, Yanrong Yang, Xiaoke Ji, Qianlin Yang, Yang Li, Jianyang Liu
Summary: A novel disassembly sequence planning method based on spatial matrices was proposed to design safer and reliable disassembly sequences for end-of-life products.
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Hang Zhao, Emmanuel Ibarboure, Vusala Ibrahimova, Ye Xiao, Elisabeth Garanger, Sebastien Lecommandoux
Summary: This research focuses on the rational design and synthesis of thermoresponsive hybrid polypeptide-polymer conjugates, which are used in combination with an artificial cytoplasm system to study the spatial organization and temperature-responsive dynamic assembly of artificial organelle structures within cell-mimicking entities.
Article
Chemistry, Analytical
Jasvir Kaur, Prabhat K. Singh
Summary: The study introduced a fluorescence turn-on probing system for monitoring ALP activity by utilizing the unique phenomenon of aggregation induced emission (AIE), demonstrating rapid, easy, sensitive and highly selective detection. The sensor showed remarkable specificity for ALP and successfully displayed potential application in human serum samples.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Biochemistry & Molecular Biology
Andrey S. Drozdov, Kristina S. Komarova, Elizaveta N. Mochalova, Elena N. Komedchikova, Victoria O. Shipunova, Maxim P. Nikitin
Summary: Introduces a method to synthesize multifunctional nanomaterials through biomimetic polymerization of dopamine derivatives. By combining magnetite nanoparticles with dopamine conjugates, multifunctional magneto-fluorescent nanocomposites were synthesized in one step. The obtained material showed excellent biocompatibility and a typical biodistribution profile for nanosized formulations. The synthesized systems were conjugated with antibodies against HER2 to improve selectivity towards HER2-positive cancer cells, allowing for dual magneto-optical in vivo studies or targeted drug delivery. This synthetic strategy can be applied to create various multifunctional hybrid nanomaterials under mild conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Tianqi Xu, Alexey Schulga, Elena Konovalova, Sara S. Rinne, Hongchao Zhang, Olga Vorontsova, Anna Orlova, Sergey M. Deyev, Vladimir Tolmachev, Anzhelika Vorobyeva
Summary: Pancreatic cancer (PC) is an aggressive malignancy, and targeted therapies could improve its treatment. Overexpression of HER3 and EpCAM in PC is associated with poor prognosis. The study investigated whether co-targeting HER3 with MM-121 and EpCAM with Ec1-LoPE could enhance therapeutic efficacy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Nataliia A. Petrunina, Alina S. Shtork, Maria M. Lukina, Vladimir B. Tsvetkov, Yuri M. Khodarovich, Alexey V. Feofanov, Anastasia M. Moysenovich, Eugene G. Maksimov, Victoria O. Shipunova, Timofei S. Zatsepin, Alexandra N. Bogomazova, Victoria O. Shender, Andrey V. Aralov, Maria A. Lagarkova, Anna M. Varizhuk
Summary: DNA-intercalated motifs serve as convenient scaffolds for designing pH-responsive nanomachines, including biocompatible pH sensors. By using a simple unimolecular dual-labeled iM scaffold and modifying it with abasic or alkyl linkers, the thermal stability and pH-induced conformational transitions of the iM were improved.
Article
Pharmacology & Pharmacy
Elena N. Komedchikova, Olga A. Kolesnikova, Ekaterina D. Tereshina, Polina A. Kotelnikova, Anna S. Sogomonyan, Alexey V. Stepanov, Sergey M. Deyev, Maxim P. Nikitin, Victoria O. Shipunova
Summary: Nanoparticle-based chemotherapy is an effective approach to cancer diagnostics and therapy, but efficient tumor targeting remains a challenge. A two-step targeted drug delivery strategy (DDS) using non-toxic and toxic modules can lower dose and systemic toxicity. In this study, we compared one-step and two-step DDS using chemotherapy loaded PLGA nanoparticles and barnase*barstar interface. We found that the two-step DDS significantly improved the performance of chemotherapy-loaded nanocarriers, making it a promising strategy for targeted anti-cancer drugs.
Article
Pharmacology & Pharmacy
Victoria O. Shipunova, Elena N. Komedchikova, Polina A. Kotelnikova, Maxim P. Nikitin, Sergey M. Deyev
Summary: Therapy for aggressive metastatic breast cancer remains a challenge, but researchers are exploring the development of chemotherapeutic nanoagents targeting cancer cell receptors. A two-step targeted delivery approach using HER2 protein and chemotherapy nanoparticles has shown to be more effective than a one-step strategy.
Article
Nanoscience & Nanotechnology
Anna S. Sogomonyan, Sergey M. Deyev, Victoria O. Shipunova
Summary: Oncotheranostic nanoagents based on PLGA nanoparticles have been developed for HER2-targeted diagnostic and photodynamic therapy. These nanoparticles can be activated by red/green light, allowing for effective imaging and treatment of HER2-positive breast cancer.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Gleb I. Tselikov, Artem Danilov, Victoria O. Shipunova, Sergey M. Deyev, Andrei V. Kabashin, Alexander N. Grigorenko
Summary: Optical biosensors have great potential in biomedical diagnostics, security, environmental, and food safety applications. However, the sensitivity of current plasmonic biosensors is limited. In this study, we propose a scissor effect in topologically dark metamaterials to achieve ultrahigh-amplitude sensitivity in biosensing events, solving the sensitivity limitation problem. By designing topologically dark metamaterials and fabricating them, we demonstrate the detection of folic acid with greatly improved sensitivity compared to previous optical counterparts.
Article
Biochemistry & Molecular Biology
Elizaveta N. Mochalova, Elena A. Egorova, Kristina S. Komarova, Victoria O. Shipunova, Nelli F. Khabibullina, Petr I. Nikitin, Maxim P. Nikitin
Summary: Recent developments in nanomedicine have introduced nanomaterials capable of recognizing and killing tumor cells with higher specificity. However, their clinical application is limited by their fast clearance from the bloodstream. MPS-cytoblockade shows promise in prolonging the circulation of nanoagents, but concerns have been raised about its potential health risks. This study suggests that the MPS-cytoblockade may be less harmful than liposomal anti-cancer drugs while significantly improving the efficacy of nanoagents.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Vera L. Kovalenko, Olga A. Kolesnikova, Maxim P. Nikitin, Victoria O. Shipunova, Elena N. Komedchikova
Summary: Photothermal therapy is a highly efficient and minimally invasive treatment for tumors, and the properties of polymeric nanoparticles (NPs) used in this therapy are affected by the synthesis components. This study explores the impact of stabilizers and solvents on the properties of PLGA NPs for photothermal therapy. By encapsulating a phthalocyanine-based photosensitizer, promising photothermal properties were achieved in PLGA NPs synthesized using mQ water as a solvent and chitosan oligosaccharide lactate as a stabilizer. The resulting composite showed photoinduced cytotoxicity against EMT6/P cells and was suitable for bioimaging.
Article
Chemistry, Multidisciplinary
Irina N. Zavestovskaya, Anton L. Popov, Danil D. Kolmanovich, Gleb V. Tikhonowski, Andrei I. Pastukhov, Maxim S. Savinov, Pavel V. Shakhov, Julia S. Babkova, Anton A. A. Popov, Ivan V. Zelepukin, Maria S. Grigoryeva, Alexander E. Shemyakov, Sergey M. Klimentov, Vladimir A. Ryabov, Paras N. Prasad, Sergey M. Deyev, Andrei V. V. Kabashin
Summary: Proton therapy is a promising radiotherapy modality for deep-seated and unresectable tumors, and its efficiency can be enhanced by using boron-containing substances. In this study, elemental boron nanoparticles (B NPs) were explored as sensitizers for proton therapy enhancement. These B NPs were efficiently absorbed by cancer cells and showed no remarkable toxicity effects. Proton beam irradiation of B NPs also led to the generation of reactive oxygen species, suggesting a possible non-nuclear mechanism of cancer cell death. Overall, this study offers a new approach with potential clinical applications for proton beam-based cancer treatment.
Article
Cell Biology
O. V. Shlepova, M. A. Shulepko, V. O. Shipunova, M. L. Bychkov, I. D. Kukushkin, I. A. Chulina, V. N. Azev, E. I. Shramova, V. A. Kazakov, A. M. Ismailova, Y. A. Palikova, V. A. Palikov, E. A. Kalabina, E. A. Shaykhutdinova, G. A. Slashcheva, E. A. Tukhovskaya, I. A. Dyachenko, A. N. Murashev, S. M. Deyev, M. P. Kirpichnikov, Z. O. Shenkarev, E. N. Lyukmanova
Summary: The study found that alpha 7-Type nicotinic acetylcholine receptor (alpha 7-nAChR) promotes the growth and metastasis of solid tumors, while Secreted Ly6/uPAR-Related Protein 1 (SLURP-1) produced by epithelial cells acts as a specific negative modulator of alpha 7-nAChR. Recombinant SLURP-1 showed antiproliferative activity in epidermoid carcinoma A431 cells, which depended on alpha 7-nAChR. Additionally, a synthetic 21 a.a. peptide mimicking SLURP-1's loop I (Oncotag) also demonstrated antitumor activity in a xenograft mice model.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Chemistry, Analytical
Stefan Jaric, Anastasiia Kudriavtseva, Nikita Nekrasov, Alexey V. Orlov, Ivan A. Komarov, Leonty A. Barsukov, Ivana Gadjanski, Petr I. Nikitin, Ivan Bobrinetskiy
Summary: Measuring NT-proBNP biomarker is recommended for preliminary diagnostics of heart failure. Recent studies have shown the possibility of early screening for biomarkers in saliva to non-invasively identify cardiac diseases. Researchers developed a label-free aptasensor using a liquid-gated field effect transistor with reduced graphene oxide monolayer and immobilized NT-proBNP specific aptamer. The biosensor demonstrated high sensitivity and responses varied depending on the ionic strength of the tested solutions. The study also showed successful performance in both diluted PBS and undiluted artificial saliva.
MICROCHEMICAL JOURNAL
(2024)
Article
Chemistry, Analytical
Alexey M. Yashchenok, Vasiliy S. Chernyshev, Elena V. Konovalova, Roman Kholodenko, Ekaterina Tsydenzhapova, Victoria O. Shipunova, Alexey A. Schulga, Sergey M. Deyev, Dmitry A. Gorin
Summary: In this study, we propose a method for the isolation and detection of sEVs based on anti-CD63 aptamer conjugated magnetic beads and the presence of membrane proteins. We compare the surface markers of EpCAM and HER2 in sEVs derived from different cell lines and blood plasma. The results show high specificity and a shorter assay time.
ANALYSIS & SENSING
(2023)