Biophysics

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Article Biochemistry & Molecular Biology

Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants -Withania somnifera(Ashwagandha),Tinospora cordifolia(Giloy) andOcimum sanctum(Tulsi) - a molecular docking study

Priya Shree, Priyanka Mishra, Chandrabose Selvaraj, Sanjeev Kumar Singh, Radha Chaube, Neha Garg, Yamini Bhusan Tripathi

Summary: By utilizing molecular docking and molecular dynamics simulation, this study identifies potential phytochemicals from medicinal plants that could inhibit SARS-CoV-2 and possess drug-like properties.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

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Article Biochemistry & Molecular Biology

Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

C. Shivanika, Deepak S. Kumar, Venkataraghavan Ragunathan, Pawan Tiwari, A. Sumitha, Brindha P. Devi

Summary: The study evaluated the potency of two hundred natural antiviral phytocompounds against the active site of the SARS-CoV-2 Main-Protease using FDA approved viral protease inhibitors as standards. Five compounds were found to be the top inhibitors for COVID-19 M(pro).

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

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Article Biochemistry & Molecular Biology

Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor

Cecylia S. Lupala, Yongjin Ye, Hong Chen, Xiao-Dong Su, Haiguang Liu

Summary: The COVID-19 pandemic caused by SARS-CoV-2 virus has resulted in over 270 million infections and 5.3 million deaths worldwide. The emergence of the Omicron variant has raised concerns about reducing vaccine efficacy and neutralizing antibodies due to its numerous mutations. Analysis indicates that the Omicron variant binds more strongly to the human ACE2 protein, with mutations at the ACE2-RBD interface enhancing tight binding through increased hydrogen bonding interactions and enlarged buried solvent accessible surface area.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2022)

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Article Biophysics

Recent advancements in optical biosensors for cancer detection

Baljinder Kaur, Santosh Kumar, Brajesh Kumar Kaushik

Summary: Optical biosensors offer rapid, real-time, portable detection with low limits and high sensitivity for diagnosing various types of cancer. Recent advancements focus on the design of biosensors utilizing resonance, scattering, chemiluminescence, luminescence, and other techniques, as well as the development of two-dimensional materials and microfabrication technologies. Surface enhanced Raman spectroscopy and terahertz waves show promise for high specificity detection, while optical fiber platforms may drive the rapid development of biosensors due to their advantages in electromagnetic interference, size, multiplexing, and remote sensing capabilities.

BIOSENSORS & BIOELECTRONICS (2022)

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Letter Biochemistry & Molecular Biology

Can AlphaFold2 predict the impact of missense mutations on structure?

Gwen R. Buel, Kylie J. Walters

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

A structural biology community assessment of AlphaFold2 applications

Mehmet Akdel, Douglas E. Pires, Eduard Porta Pardo, Jurgen Janes, Arthur O. Zalevsky, Balint Meszaros, Patrick Bryant, Lydia L. Good, Roman A. Laskowski, Gabriele Pozzati, Aditi Shenoy, Wensi Zhu, Petras Kundrotas, Victoria Ruiz Serra, Carlos H. M. Rodrigues, Alistair S. Dunham, David Burke, Neera Borkakoti, Sameer Velankar, Adam Frost, Jerome Basquin, Kresten Lindorff-Larsen, Alex Bateman, Andrey Kajava, Alfonso Valencia, Sergey Ovchinnikov, Janani Durairaj, David B. Ascher, Janet M. Thornton, Norman E. Davey, Amelie Stein, Arne Elofsson, Tristan Croll, Pedro Beltrao

Summary: This study evaluates the performance of AlphaFold2 in structural biology applications and finds that it performs well and can partially replace experimentally determined structures, which is of great significance for life science research.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach

Abdus Samad, Foysal Ahammad, Zulkar Nain, Rahat Alam, Raihan Rahman Imon, Mahadi Hasan, Md Shahedur Rahman

Summary: The ongoing COVID-19 outbreak poses a significant challenge to global public health security. In this study, a multi-epitope vaccine against SARS-CoV-2 was designed using an immunoinformatics approach. The vaccine showed antigenicity, immunogenicity, and non-allergenicity, with suitable physicochemical properties. Molecular dynamics simulation and immune simulation demonstrated the effectiveness of the vaccine, and codon optimization was performed. This designed peptide vaccine has the potential to be an excellent prophylactic candidate against SARS-CoV-2.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

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Article Biochemistry & Molecular Biology

Aquaporin 8ab is required in zebrafish embryonic intestine development

Shiping Wang, Yinyin Qin, Jiajing Sheng, Xuchu Duan, Lizong Shen, Dong Liu

Summary: AQP8 is highly expressed in the gastrointestinal tract of mammals, potentially playing a role in its physiological and pathological processes. In zebrafish, three types of aqp8s are encoded in the genome, with aqp8ab mainly expressed in the embryonic intestine. Knocking out aqp8ab leads to defects in intestine development and abnormal formation of the intestinal lumen.

ACTA BIOCHIMICA ET BIOPHYSICA SINICA (2022)

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Article Biochemistry & Molecular Biology

Carbon nanotube field-effect transistor (CNT-FET)-based biosensor for rapid detection of SARS-CoV-2 (COVID-19) surface spike protein S1

Mazin A. Zamzami, Gulam Rabbani, Abrar Ahmad, Ahmad A. Basalah, Wesam H. Al-Sabban, Saeyoung Nate Ahn, Hani Choudhry

Summary: A fast, easy-to-use, low-cost, and quantitative electrochemical biosensor based on CNT-FET has been developed for quick and accurate detection of SARS-CoV-2 S1 antigen in fortified saliva samples. The biosensor exhibits high sensitivity, selectivity, and can save time, making it a valuable platform for rapid detection of SARS-CoV-2 S1 antigen from patient saliva.

BIOELECTROCHEMISTRY (2022)

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Article Biophysics

2D metal carbides and nitrides (MXenes) for sensors and biosensors

Subbiah Alwarappan, Noel Nesakumar, Dali Sun, Tony Y. Hu, Chen-Zhong Li

Summary: MXenes, as a type of two-dimensional layered material, has attracted great attention due to its interesting properties. This review covers the synthesis routes, surface functionalization, and modification strategies of MXenes, as well as the development of gas, electrochemical, and optical biosensors based on MXenes.

BIOSENSORS & BIOELECTRONICS (2022)

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Editorial Material Cell & Tissue Engineering

A Conversation on Artificial Intelligence, Chatbots, and Plagiarism in Higher Education

Michael R. King

CELLULAR AND MOLECULAR BIOENGINEERING (2023)

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Article Biophysics

Aptamer-based electrochemical biosensor for rapid detection of SARS-CoV-2: Nanoscale electrode-aptamer-SARS-CoV-2 imaging by photo-induced force microscopy

Juan Carlos Abrego-Martinez, Maziar Jafari, Siham Chergui, Catalin Pavel, Diping Che, Mohamed Siaj

Summary: Quick and accurate diagnosis of the COVID-19 is crucial in stopping the spread of the virus. The development of an aptamer-based biosensor on a screen-printed carbon electrode platform shows promise in providing rapid and sensitive detection of SARS-CoV-2, offering a potential solution to the current challenges in COVID-19 diagnosis.

BIOSENSORS & BIOELECTRONICS (2022)

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Article Biochemistry & Molecular Biology

Fabrication of Cu2MoS4 decorated WO3 nano heterojunction embedded on chitosan: Robust photocatalytic efficiency, antibacterial performance, and bacteria detection by peroxidase activity

Haitao Lin, Tao Li, Baadal Jushi Janani, Ali Fakhri

Summary: Cu2MoS4/WO3 supported on chitosan was prepared by precipitation method and used in photocatalyst, antibacterial agent, and biosensor applications. The nanocomposites showed effective photocatalysis activity under visible light conditions and exhibited antibacterial activity against G+/- bacteria.

JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY (2022)

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Article Biophysics

A smartphone-based visual biosensor for CRISPR-Cas powered SARS-CoV-2 diagnostics

Long Ma, Lijuan Yin, Xiaoyan Li, Si Chen, Lei Peng, Guozhen Liu, Shengying Ye, Wenlu Zhang, Shuli Man

Summary: Researchers have developed a CRISPR-Cas12a powered biosensor for ultra-sensitive and selective detection of SARS-CoV-2, with smartphone readout capability. The biosensor showed excellent performance in detecting synthetic vectors, transcribed RNA, and pseudoviruses, providing 100% agreement with qPCR results when tested with clinical samples. It offers a novel and robust technology for clinically sensitive detection of SARS-CoV-2.

BIOSENSORS & BIOELECTRONICS (2022)

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Article Biophysics

Wearable biosensors for real-time sweat analysis and body motion capture based on stretchable fiber-based triboelectric nanogenerators

Tianming Zhao, Yongming Fu, Chuxiao Sun, Xishan Zhao, Chunxiao Jiao, An Du, Qi Wang, Yupeng Mao, Baodan Liu

Summary: Wearable biosensors based on stretchable fiber-based triboelectric nanogenerators (F-TENG) allow for real-time sweat analysis and body motion capture. These devices are self-powered and exhibit high response rates, making them promising for various applications in the Internet of Things (IoT).

BIOSENSORS & BIOELECTRONICS (2022)

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Article Biophysics

DIMENSION: Dynamic MR imaging with both k-space and spatial prior knowledge obtained via multi-supervised network training

Shanshan Wang, Ziwen Ke, Huitao Cheng, Sen Jia, Leslie Ying, Hairong Zheng, Dong Liang

Summary: This paper proposes a dynamic MR imaging method, named DIMENSION, which integrates both k-space and spatial prior knowledge via multi-supervised network training. It achieves improved reconstruction results in shorter time.

NMR IN BIOMEDICINE (2022)

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Article Biochemistry & Molecular Biology

Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2: an in silico approach to combat COVID-19

Ananta Swargiary, Shafi Mahmud, Md. Abu Saleh

Summary: COVID-19 and its causative organism SARS-CoV2 have brought significant challenges to global health. This study utilized in-silico techniques to screen plant-derived compounds and identified amentoflavone and gallocatechin gallate as potential inhibitors of the SARS-CoV2 proteases.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

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Article Biophysics

Indications for haematopoietic cell transplantation for haematological diseases, solid tumours and immune disorders: current practice in Europe, 2022

John A. Snowden, Isabel Sanchez-Ortega, Selim Corbacioglu, Grzegorz W. Basak, Christian Chabannon, Rafael de la Camara, Harry Dolstra, Rafael F. Duarte, Bertram Glass, Raffaella Greco, Arjan C. Lankester, Mohamad Mohty, Benedicte Neven, Regis Peffault de Latour, Paolo Pedrazzoli, Zinaida Peric, Ibrahim Yakoub-Agha, Anna Sureda, Nicolaus Kroeger

Summary: The EBMT has updated recommendations on indications for HCT and encourages harmonization of practice to aggregate experience. JACIE accreditation standards and reference to COVID-19 guidance are recommended for decision making.

BONE MARROW TRANSPLANTATION (2022)

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Article Biochemistry & Molecular Biology

Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases

Banoth Karan Kumar, Faheem, Kondapalli Venkata Gowri Chandra Sekhar, Rupal Ojha, Vijay Kumar Prajapati, Aravinda Pai, Sankaranarayanan Murugesan

Summary: This study identified potential ligands that may act as inhibitors of SARS-CoV-2 M-pro through computational screening. The molecules SN00293542 and SN00382835 showed the highest docking scores and demonstrated stability through molecular dynamics studies.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

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Article Biochemistry & Molecular Biology

Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: anin silicodocking and molecular dynamics simulation approach

Ranabir Majumder, Mahitosh Mandal

Summary: This study investigates potential inhibitors of COVID-19 M(pro) and screens out several natural compounds through virtual molecular docking and molecular dynamics simulation. The results show that these natural compounds have high binding affinity to COVID-19 M(pro) and possess important dynamic properties such as stability and flexibility. However, further preclinical and clinical trials are needed to validate these compounds.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

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