Article
Biochemical Research Methods
Gabriele Antonio Zingale, Alessia Distefano, Irene Pandino, Nunzio Tuccitto, Valentina Oliveri, Massimiliano Gaeta, Alessandro D'Urso, Alfio Arcoria, Giuseppe Grasso
Summary: In the field of conformational diseases, monitoring peptide and protein aggregation is crucial for understanding physiological pathways and pathological processes. A new experimental method based on the fluorescent properties of carbon dots upon protein binding is introduced to monitor protein aggregation. The proposed methodology allows for monitoring the initial stages of insulin aggregation under different experimental conditions without potential disturbances or molecular probes.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Astronomy & Astrophysics
Maria Cristina Fortuna, Henk Hoekstra, Benjamin Joachimi, Harry Johnston, Nora Elisa Chisari, Christos Georgiou, Constance Mahony
Summary: This study investigates the impact of different galaxy samples on cosmic shear studies using the halo model formalism, accounting for varied IA features and redshift dependencies. The model includes luminosity and signal radial dependencies, and uses realistic mocks to validate predictions. Results indicate that uncertainties in predicting IA signal largely stem from fainter galaxies.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Review
Chemistry, Multidisciplinary
Yulun Wu, Huangxu Li, Tiancheng Liu, Ming Xu
Summary: This review comprehensively examines the use of proteins and their subunits in addressing engineering issues in various rechargeable batteries. The latest advances in electrode, electrolyte, separator, and other components are discussed, with a particular emphasis on the impact of biomolecules on electrochemical properties.
ADVANCED MATERIALS
(2023)
Article
Multidisciplinary Sciences
Sonia T. Nicolaou, Max Hebditch, Owen J. Jonathan, Chandra S. Verma, Jim Warwicker
Summary: Charge plays a crucial role in determining the properties of intrinsically disordered proteins and regions. Phosphorylation can alter the charge distribution, which is visualized by the PhosIDP web tool. Understanding the modulation of charge by phosphorylation can lead to functional insights for these proteins.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Ana M. Diez-Pascual, Abbas Rahdar
Summary: This review provides an overview of polyelectrolytes (PEs) research and applications. PE films prepared by layer-by-layer (LbL) approach offer precise control over properties and have wide biomedical applications. The review highlights the design and fabrication research of nanofilms and discusses their applications in the biomedical field.
Article
Materials Science, Biomaterials
Kailash Prasad Prajapati, Masihuzzaman Ansari, Deepak Kumar Yadav, Shikha Mittal, Bibin Gnanadhason Anand, Karunakar Kar
Summary: Covalent tagging of fluorophores is crucial for studying biological processes and has advantages despite challenges in synthesis and purification. A novel method for making fluorescent amyloid nanofibers is described, which maintains the characteristics of the nanofibers and exhibits stability. This method has significant implications for amyloid research in vitro and in animal models.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Physical
Max Lukas, Ralph Schwidetzky, Anna T. Kunert, Ellen H. G. Backus, Ulrich Poeschl, Janine Froehlich-Nowoisky, Mischa Bonn, Konrad Meister
Summary: Ice-nucleating proteins (INPs) from bacteria are highly effective at initiating ice formation near 0 degrees C. Research shows that INPs have a defined solution structure and do not undergo significant conformational changes upon cooling, but irreversible structural changes occur upon heating. Sum-frequency generation (SFG) spectroscopy reveals that active and heat-inactivated INPs have similar effects on ordering interfacial water molecules during cooling.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Adeola Shobo, Alexander Roentgen, Mark A. Hancock, Gerhard Multhaup
Summary: This study compared the properties of synthetic A beta 42 from different vendors with recombinant A beta 42 using various experimental methods. It found that recombinant A beta 42 provided a reproducible mimetic of desired properties, and the combined use of MALDI-MS and CD could predict the bioactivity of A beta 42.
Article
Biochemistry & Molecular Biology
Susanna Navarro, Salvador Ventura
Summary: Protein aggregation is associated with diseases and industrial production. This article reviews computational tools for predicting and identifying protein aggregation.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Li Xue, Dehao Yu, Jing Sun, Liangyu Guan, Chengzhi Xie, Luo Wang, Yuanyuan Jia, Junyu Tian, Heli Fan, Huabing Sun
Summary: We report four coumarin-maleimide probes for fast detection of GSH and labeling peptides/proteins. These probes react with GSH via Michael addition, leading to a significant increase in fluorescence quantum yield. Optimized probe 4 is capable of detecting GSH in vitro and in vivo, and the method can be extended for fluorescent labeling of peptides/proteins and tracking their cellular uptake process.
Article
Biochemical Research Methods
Tohru Yamagaki, Tsukiho Osawa, Kohki Fujikawa, Takehiro Watanabe, Kohtaro Sugahara
Summary: The reactivity of alkaloids in dehydrogenation was studied using mass spectrometry, and the relationship between reactivity and chemical properties/structures of alkaloids was explored. It was found that different types of alkaloids exhibited different characteristics in dehydrogenation reactions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Multidisciplinary
Songtao Ye, Han Zhang, Jinyu Fei, Charles H. Wolstenholme, Xin Zhang
Summary: By chemically installing extended pi-rich alternating carbon-carbon linkages between the rotational electron donors and acceptors of RBFs, the lack of control of their viscosity sensitivity has been resolved. The length of the linkage strongly influences the viscosity sensitivity, providing the possibility to design RBFs with different viscosity sensitivities. RBFs can differentiate misfolded protein oligomers and insoluble aggregates in test tubes and live cells through a dual-color imaging strategy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Zhiwei Huang, Huajian Lin, Shujuan Yu, Hanlin Li, Yang Zhou, Yuan Cheng, Shanli Chen, Cai Yuan, Mingdong Huang
Summary: Genetic fusion of human serum albumin with peptides is an important strategy to enhance the lifespan of peptides in the bloodstream. A study found that inserting a peptide into residue 363-364 of albumin can maintain the activity of the peptide. Internal fusion of the protein has a stronger inhibitory effect compared to fusion at the N-terminus, without affecting albumin expression, secondary structure, and inherent drug binding activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Materials Science, Multidisciplinary
Ananya Renuka Balakrishna, Richard D. James
Summary: This study develops a theoretical and computational tool to investigate the interplay between material constants that govern coercivity in bulk magnetic alloys. The interactions between local instabilities and material constants, such as anisotropy and magnetostriction constants, are identified as key factors in governing magnetic coercivity. The study provides a theoretical framework to potentially discover novel magnetic materials with low coercivity.
Article
Biochemical Research Methods
Aman Chandra Kaushik, Aamir Mehmood, Gurudeeban Selvaraj, Xiaofeng Dai, Yi Pan, Dong-Qing Wei
Summary: The novel coronavirus (COVID-19) has become a global pandemic, requiring urgent vaccine development. The CoronaPep tool is designed to quickly identify anti-coronavirus targets and provide precise anti-viral peptides, which can aid researchers in oncology and drug design.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Telecommunications
Sandeep Kumar, Puspraj Singh Chauhan, Manpreet Kaur, Tarun Lata
Summary: This paper studies the effective capacity performance of a delay-sensitive communication system over a cascaded Rayleigh fading channel with arbitrary correlation. Closed-form mathematical expressions for the effective capacity are derived, and the effect of different fading parameters on the system's effective throughput is demonstrated.
WIRELESS PERSONAL COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Giuseppe Licari, Kyle P. Martin, Maureen Crames, Joseph Mozdzierz, Michael S. Marlow, Anne R. Karow-Zwick, Sandeep Kumar, Joschka Bauer
Summary: Adequate stability, manufacturability, and safety are crucial in bringing antibody-based biotherapeutics to the market. This study introduces a physicochemical description of 91 market-stage antibody-based biotherapeutics based on molecular properties of variable regions. The evaluation includes molecular dynamics simulations to assess conformational flexibility and the impact of different conditions on molecular interactions. A computational tool called DENIS is proposed to compare biotherapeutic candidates and predict their properties in aqueous environments.
MOLECULAR PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
Vanishree S. Bhat, Marichandran Vadivel, Dharmendra Pratap Singh, V. A. Raghunathan, Arun Roy, Sandeep Kumar
Summary: In this study, a series of novel nitrogen and oxygen-incorporated chromenonaphthophenanthridine-based elliptical dimers were synthesized through tandem Pictet-Spengler cyclization followed by ipso-aromatic substitution in one-pot. Their mesophase characteristics were characterized by optical microscopy, differential scanning calorimetry, and X-ray diffraction studies. The photophysical properties were investigated using UV-vis and emission spectroscopy, and the charge transport properties were analyzed by time-of-flight measurements, with observed ambipolar mobilities of the order of 10(-3) cm(2) V-1 s(-1). These materials show promising potential for applications in organic electronics due to their high solubility, excellent thermal stability, self-organizing properties, and ambipolar charge transport characteristics.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Engineering, Electrical & Electronic
Dimpal Janu, Sandeep Kumar, Kuldeep Singh
Summary: GCN-CSS is a novel Graph Convolution Network-based cooperative spectrum sensing methodology that adapts to the dynamic changes in the Cognitive Radio Network. The proposed model is proven to be superior in different dynamic scenarios of the wireless environment through sufficient simulations.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2023)
Article
Engineering, Electrical & Electronic
Khalid K. Almuzaini, Shalini Stalin, Sindhu P. Menon, Sandeep Kumar, Stephen Ojo, Prashant Kumar Shukla, Piyush Kumar Pareek, Piyush Kumar Shukla
Summary: In wireless sensor networks, the challenge lies in designing and managing the networks considering limited power, stringent bandwidth, dynamic topology, and high network density. The proposed IGRPSO protocol addresses these challenges by optimizing routing with minimal latency and a higher packet delivery ratio.
INTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS
(2023)
Review
Pharmacology & Pharmacy
Saurabh Shah, Ramesh Joga, Tejaswini Kolipaka, Chetan Sabnis Dushyantrao, Pooja Khairnar, Vivek Phatale, Giriraj Pandey, Saurabh Srivastava, Sandeep Kumar
Summary: This article introduces the liquid crystalline phase, which has attracted global attention due to its intriguing properties. It enumerates the different classes of liquid crystals and focuses on lyotropic liquid crystals (LLCs), which exhibit their liquid crystalline nature based on the surrounding solvent media. The article discusses the advantages of LLCs in drug delivery and tissue regeneration, fabrication techniques, and applications in novel therapeutic avenues.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
T. Aravinda, Srilatha Rao, A. S. Sowmyashree, Ashwathanarayana Gowda, L. Parashuram, Kayim Pineda Urbina, Gururaj Kudur Jayaprakash, Sandeep Kumar
Summary: In this study, a metal-free phthalocyanine-based discotic liquid crystal (PcDLC) was tested for its corrosion inhibitory capacity on mild steel (MS) samples in 1.0 M HCl medium using potentiodynamic and electrochemical impedance parameters. The PcDLC exhibited excellent corrosion inhibition with a maximum efficiency of 89.61%. The strong adsorption of PcDLC onto the MS surface was responsible for this superior ability. Scanning electron microscopy and FTIR confirmed the formation of a protective layer of inhibitors on the MS surface. Density function theory revealed a strong interaction between the inhibitor and surface iron atoms.
Article
Chemistry, Multidisciplinary
Dharmendra Pratap Singh, Asmita Shah, Indu Bala, Vadivel Marichandran, Santanu Kumar Pal, Abhishek Kumar Srivastava, Sandeep Kumar
Summary: This article presents the charge transport and organic electronic applications of naphthophenanthridine derivatives and a dimer composed of pentaalkynylbenzene and triphenylene discotic liquid crystals. The investigated compounds exhibit high ambipolar charge carrier mobility, making them suitable for fabricating organic semiconducting electronic devices.
Review
Medicine, Research & Experimental
Monica L. Fernandez-Quintero, Anne Ljungars, Franz Waibl, Victor Greiff, Jan Terje Andersen, Torelif T. T. Gjolberg, Timothy P. P. Jenkins, Bjorn Gunnar Voldborg, Lise Marie Grav, Sandeep Kumar, Guy Georges, Hubert Kettenberger, Klaus R. R. Liedl, Peter M. M. Tessier, John McCafferty, Andreas H. H. Laustsen
Summary: Beyond potency, a good developability profile is essential for a biological drug. Early selection and screening for these attributes can save resources and avoid costly failures. This review highlights key developability properties, such as the source, biophysical and pharmacokinetic properties, and recombinant expression, and discusses methods for identifying molecules with liabilities and optimizing drug leads. The article also compares developability parameters for injectable and orally delivered biologics and provides an outlook on emerging trends in biologics development.
Review
Medicine, Research & Experimental
Kyle P. P. Martin, Christine Grimaldi, Rolf Grempler, Steven Hansel, Sandeep Kumar
Summary: There is significant interest in antibody-based biotherapeutics due to their selectivity and desirable pharmacology. This study analyzed characteristics of 89 marketed antibody-based biotherapeutics approved between 1986 and mid-2020. The findings reveal major trends in their emergence as best-selling pharmaceuticals and provide insights for better drug discovery and development strategies.
Article
Geriatrics & Gerontology
Sagar Vyavahare, Sandeep Kumar, Kathryn Smith, Bharati Mendhe, Roger Zhong, Marion A. Cooley, Babak Baban, Carlos M. Isales, Mark Hamrick, William Hill, Sadanand Fulzele
Summary: Emerging evidence suggests that microRNA-141-3p plays a role in age-related pathologies. In this study, we inhibited miR-141-3p expression in aged mice and observed improved immune, bone, and muscle health. Treatment with Anti-miR-141-3p resulted in decreased pro-inflammatory cytokines, a shift from pro-inflammatory to anti-inflammatory immune cell populations, and improved bone microstructure and muscle fiber size. Molecular analysis revealed the role of miR-141-3p in regulating senescence and inflammation, as well as its potential crosstalk with FOXO-1 transcription factor. These findings suggest that inhibiting miR-141-3p may be a potential strategy for promoting healthy aging.
Article
Geriatrics & Gerontology
Mohini Gharpure, Jie Chen, Resheek Nerella, Sagar Vyavahare, Sandeep Kumar, Carlos M. Isales, Mark Hamrick, Satish Adusumilli, Sadanand Fulzele
Summary: Sarcopenia, a condition characterized by decreased muscle mass, altered muscle composition, and reduced muscle strength, disproportionately affects males and females with age. This study identified differentially regulated genes in aged skeletal muscle from males and females, with 269 genes showing at least a twofold expression difference. Gene Ontology analysis revealed distinct pathways involved in aged female and male skeletal muscle, suggesting the potential for sex-specific therapeutic targets to combat sarcopenia and promote healthy aging.
Article
Telecommunications
Dimpal Janu, Kuldeep Singh, Sandeep Kumar, Sandeep Mandia
Summary: In this letter, a hierarchical cooperative LSTM network-based CSS method is proposed, which utilizes CNN and LSTM network. The CNN extracts spatial features from input CMs generated by sensing data of each SU, and the sequence of spatial features is fed into SU-LSTM to learn the PU activity pattern at SU level. The cooperative LSTM learns the group-level PU activity pattern from all SU-level temporal feature representations. The effectiveness of the proposed method is proven through sufficient simulations, outperforming the state-of-the-art in terms of detection probability and classification accuracy.
IEEE COMMUNICATIONS LETTERS
(2023)
Article
Biochemical Research Methods
Asif Khan, Alexander I. Cowen-Rivers, Antoine Grosnit, Derrick-Goh-Xin Deik, Philippe A. Robert, Victor Greiff, Eva Smorodina, Puneet Rawat, Rahmad Akbar, Kamil Dreczkowski, Rasul Tutunov, Dany Bou-Ammar, Jun Wang, Amos Storkey, Haitham Bou-Ammar
Summary: Antibodies are proteins capable of specific molecular recognition. The CDRH3 region of the antibody plays a crucial role in antigen-binding specificity. Designing optimal antigen-specific CDRH3 is important for therapeutic antibody development. In this study, we present AntBO, a Bayesian optimization framework that utilizes a CDRH3 trust region for in silico antibody design with favorable developability scores. Our results demonstrate that AntBO outperforms experimentally obtained CDRH3s and can identify high-affinity CDRH3 sequences with minimal protein designs and no domain knowledge.
CELL REPORTS METHODS
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)