Review
Biochemistry & Molecular Biology
Megan H. Wright
Summary: This review highlights the importance of chemical biology in studying cell-cell communication, focusing on the applications of chemical tools for protein labeling, signal pathway analysis, and protein-protein interaction discovery.
BIOCHEMICAL JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Sajad Najafi, Seyed Mohsen Aghaei Zarch, Jamal Majidpoor, Safoora Pordel, Shahin Aghamiri, Mohammed Fatih Rasul, Yahya Asemani, Omid Vakili, Vida Mohammadi, Ahmad Movahedpour, Nahid Arghiani
Summary: Circular RNAs (circRNAs) are a new class of non-coding RNAs with a closed loop structure, resistant to degrading enzymes, and suggested to have regulatory roles in gene expression. In the human brain, circRNAs show abundance, dynamic expression, and regulation, and are believed to be involved in brain functions and related diseases. They have demonstrated differential expression in brain compartments and contribute to CNS development. Additionally, circRNAs are associated with key pathways involved in brain development, such as axon guidance and signaling pathways.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Chemistry, Multidisciplinary
Aurora Rizzo, Andrea Listorti, Silvia Colella
Summary: This article discusses the impact of ink evolution on the performance of metal halide perovskite solar cells, emphasizing the importance of understanding ink properties for industrialization. The article highlights that even small changes in ink composition can greatly affect photovoltaic performances.
Review
Cell Biology
Xin Liu, Yuping Du, Zhenghao Huang, Honglei Qin, Jingwen Chen, Yang Zhao
Summary: N6-Methyladenosine (m6A) is a common and endogenous modification of eukaryotic RNAs, playing important roles in RNA metabolism, cell differentiation, cell circadian rhythm, and cell cycle. The methyltransferase-like enzyme 14 (METTL14) functions as an RNA-binding scaffold in the MTC, promoting RNA substrate recognition and enhancing the catalytic capability of METTL3.
CELL PROLIFERATION
(2022)
Article
Plant Sciences
Octavio Martinez, Magda L. Arce-Rodriguez, Fernando Hernandez-Godinez, Christian Escoto-Sandoval, Felipe Cervantes-Hernandez, Corina Hayano-Kanashiro, Jose J. Ordaz-Ortiz, M. Humberto Reyes-Valdes, Fernando G. Razo-Mendivil, Ana Garces-Claver, Neftali Ochoa-Alejo
Summary: This study compared the gene expression profiles of domesticated and wild chili pepper ancestors during fruit development, revealing significant differences in cell cycle gene expression between them, possibly driven by selection pressures during domestication. Domesticated genotypes showed higher gene expression levels and earlier peaks.
Article
Biology
Yulong Liu, Michelle E. Kossack, Matthew E. McFaul, Lana N. Christensen, Stefan Siebert, Sydney R. Wyatt, Caramai N. Kamei, Samuel Horst, Nayeli Arroyo, Iain A. Drummond, Celina E. Juliano, Bruce W. Draper, John Postlethwait
Summary: Zebrafish are important in studying vertebrate tissue and organ development, but there are still gaps in our understanding of genes that regulate gonad development and reproduction. Single-cell RNA sequencing has provided novel insights into zebrafish ovarian development and function by identifying cell subpopulations and their functional significance.
Article
Plant Sciences
Chen Sheng, Shengnan Song, Wangyi Zhou, Senouwa Segla Koffi Dossou, Rong Zhou, Yanxin Zhang, Donghua Li, Jun You, Linhai Wang
Summary: This study conducted a comprehensive transcriptome analysis on two sesame varieties and identified key genes related to plant height development. The regulatory network controlling plant height was revealed, providing valuable genetic resources for optimizing plant architecture in sesame.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Review
Chemistry, Inorganic & Nuclear
Hongdong Shi, Yi Wang, Simin Lin, Jingxue Lou, Qianling Zhang
Summary: Iridium complexes are widely used as molecular sensors due to their rich photophysical properties, such as large Stokes shifts, long emission lifetimes, environment-sensitive emissions, and high luminescence quantum yields. This paper reviews the recent development and application of iridium complexes as probes for various substances, and discusses the outlook for iridium-based probes.
DALTON TRANSACTIONS
(2021)
Article
Biochemistry & Molecular Biology
Alyson M. Curry, Elizabeth Barton, Wenjia Kang, Daniel V. Mongeluzi, Yana Cen
Summary: This study developed simple activity-based chemical probes for investigating active sirtuin content and successfully enabled cell imaging of sirtuin activity change, providing new tools for future drug discovery strategies.
Review
Materials Science, Multidisciplinary
Jinglu Liu, Yiran Ding, Mengqi Zeng, Lei Fu
Summary: Two-dimensional quantum materials have novel quantum functions and potential applications due to their unique physical and chemical properties. Understanding the design and synthesis of these materials is crucial for studying their intrinsic quantum physics and exploring their potential properties and applications.
Article
Engineering, Environmental
Amanda Larasati, Geoffrey D. Fowler, Nigel J. D. Graham
Summary: Granular activated carbon adsorption is widely used for the removal of contaminants in water, requiring periodic regeneration. Chemical regeneration is identified as an effective alternative, but a suitable regenerant solution for a wide range of contaminants has not been identified yet.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Agronomy
Yuanxin Qiu, Zexiong Zhang, Dongjie Liu, Jianliang Liu, Qin Wang, Qian Yu, Le Zhong, Hongfeng Xie
Summary: This study compared fruits grown through new planting methods (black bags combined with bio-organic fermentation fertilizer) and conventional planting methods (using a chemical fertilizer without bagging). It was found that the new planting methods significantly improved the fruit quality in terms of weight, hardness, and sugar content. RNA sequencing analysis revealed that the new cultivation technology promoted soluble sugar accumulation and cell-wall synthesis through molecular regulation, which improved the sweetness and sensory quality of the fruit.
Article
Chemistry, Multidisciplinary
Luisina Rodriguez, Andres Lopez, Guillermo Moyna, Gustavo A. Seoane, Danilo Davyt, Aprimelvaro Vazquez, Gonzalo Hernandez, Ignacio Carrera
Summary: This study analyzed the composition of ayahuasca samples using NMR and LC-MS/MS techniques, revealing the presence of fructose in addition to major alkaloids. Harmine and other alkaloids were found in the suspended solids for the first time, shedding new light on the components of the psychedelic beverage.
Article
Biochemistry & Molecular Biology
Madhura N. Paranjpe, Valeria Marina, Aleksandr A. Grachev, Tinashe P. Maviza, Olga A. Tolicheva, Alena Paleskava, Ilya A. Osterman, Petr Sergiev, Andrey L. Konevega, Yury S. Polikanov, Matthieu G. Gagnon
Summary: Thermorubin (THR) is an antibiotic that can inhibit translation initiation and disrupt tRNA accommodation in the ribosomal A site, causing ribosome stalling at internal and termination codons. Our findings reveal that THR affects multiple steps of translation elongation and can coexist with P- and A-site tRNAs, allowing ribosomes to continue elongation in the presence of the drug.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Chemistry, Multidisciplinary
Chengyi Hu, Ruihao Chen, Nanfeng Zheng
Summary: The interfaces between inorganic functional nanomaterials and their surface modifiers are crucial in determining their properties. Strategies to design model inorganic nanomaterials with well-defined interfaces can simplify the investigation of interfacial effects on performance enhancement. Atomically precise metal nanoclusters and ultrathin low-dimensional nanomaterials modified with organic ligands help understand how interfacial effects influence catalysis.
ADVANCED MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Anita Donlic, Martina Zafferani, Giacomo Padroni, Malavika Puri, Amanda E. Hargrove
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Matthew J. Henley, Brian M. Linhares, Brittany S. Morgan, Tomasz Cierpicki, Carol A. Fierke, Anna K. Mapp
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Jesse Davila-Calderon, Neeraj N. Patwardhan, Liang-Yuan Chiu, Andrew Sugarman, Zhengguo Cai, Srinivasa R. Penutmutchu, Mei-Ling Li, Gary Brewer, Amanda E. Hargrove, Blanton S. Tolbert
NATURE COMMUNICATIONS
(2020)
Article
Radiology, Nuclear Medicine & Medical Imaging
Natalie K. Domeisen, Jordan E. Forte, Victor K. Agwu, Samuel C. Allen, Nikki A. Mehran, Tebianne Abubaker, Nishk P. Patel, Niobra M. Keah, Yolanda Shaw, Frederick S. Jones, Carol P. Geer, Kevin D. Hiatt
Summary: The Radiology Scholars Certificate Program (RSCP) is an extracurricular program designed to address disparities in radiology education and exposure during medical school.
ACADEMIC RADIOLOGY
(2022)
Article
Chemistry, Medicinal
Zhengguo Cai, Martina Zafferani, Olanrewaju M. Akande, Amanda E. Hargrove
Summary: The determination of high-resolution RNA structures and the recognition of RNA by small molecules have been challenging in the field of RNA therapeutics. In this study, QSAR models were developed to predict both thermodynamic and kinetic binding parameters of small molecules and HIV-1 TAR RNA. These models allowed for the direct interpretation of critical properties for binding strength and kinetic rate constants and were validated and compared to other methods, demonstrating their accuracy and general applicability.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Martina Zafferani, Justin G. Martyr, Dhanasheel Muralidharan, Nadeska I. Montalvan, Zhengguo Cai, Amanda E. Hargrove
Summary: The characterization of RNA tertiary structures in human diseases has shown their pervasiveness and potential therapeutic value. This study focuses on small molecule-mediated modulation of RNA tertiary structures, specifically targeting the triple helix of the noncoding RNA MALAT1. Through a series of assays, the researchers identified small molecules that can bind to and impact the stability of the MALAT1 triple helix. They also developed predictive models for evaluating small molecule affinity and stability-based assays. This work establishes a powerful tool for studying and targeting disease-associated RNA triple helices.
ACS CHEMICAL BIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Greta Bagnolini, TinTin B. Luu, Amanda E. Hargrove
Summary: RNA structures play a crucial role in biology and disease, but there is a lack of small molecule chemical probes or drugs that can regulate these functions. Machine learning and computational methods have the potential to overcome the challenges in RNA targeting and have already identified important factors for selective recognition in RNA:small molecule complexes. These tools can aid in the rational design of small molecules for specific RNA targets. This perspective highlights the value of using machine learning and computational methods to advance RNA:small molecule targeting.
Article
Biochemistry & Molecular Biology
Jennifer Voegele, Daniel Hymon, Jason Martins, Jan Ferner, Hendrik R. A. Jonker, Amanda E. Hargrove, Julia E. Weigand, Anna Wacker, Harald Schwalbe, Jens Woehnert, Elke Duchardt-Ferner
Summary: This study presents the high-resolution structure of stem-loop 4 (5_SL4) in the 5'-untranslated region of the SARS-CoV-2 genome using solution state nuclear magnetic resonance spectroscopy. The structure of 5_SL4 exhibits an extended rod-like shape with a flexible looped-out nucleotide and two mixed tandem mismatches. These non-canonical elements disrupt the stem-loop structure locally and are highly conserved among different variants of SARS-CoV-2. Small molecule ligands can bind to 5_SL4 with intermediate affinity near these non-canonical elements.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Martina Zafferani, Dhanasheel Muralidharan, Nadeska Montalvan, Amanda E. Hargrove
Summary: The increasing understanding of RNA tertiary structures in human diseases has led to the need for decoding their functions and developing therapeutic interventions. However, there are limited examples of small molecules that target these structures. To address this, researchers have developed a high-throughput screening platform to assess the stability of RNA triple helices and explore the impact of mutations and small molecules. This approach can significantly accelerate the discovery of probes that modulate RNA structures and provide insights into their roles.
RSC CHEMICAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Aline Umuhire Juru, Amanda E. Hargrove
Summary: Since the discovery of mRNA in 1961, our understanding of the roles of RNA molecules has significantly increased. RNA molecules not only serve as a link between DNA and proteins, but also play direct effector roles by binding to various ligands. As a result, the misregulation of RNA molecules is often associated with disease phenotypes, making them potential targets for drug development efforts.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Martina Zafferani, Amanda E. Hargrove
Summary: The development of small molecule ligands for non-coding RNAs shows therapeutic potential, with recent advances in technique enabling the identification of complex RNA structures and the design of selective molecules. Targeting RNA tertiary and quaternary structures with small molecules presents promising opportunities for treating human diseases.
CELL CHEMICAL BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
James P. Falese, Anita Donlic, Amanda E. Hargrove
Summary: This article reviews recent advances in understanding RNA biology, including its crucial roles in various disease states and the challenges and methods for drug design targeting RNA. It focuses on discussing RNA structural hierarchy, functional classes, and dynamics, as well as methods for small molecule screening and RNA structure determination. Finally, it summarizes the unique challenges and emerging solutions for generating RNA-targeted ligands from both RNA and small molecule perspectives.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Chemistry, Multidisciplinary
Amanda E. Hargrove
CHEMICAL COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
G. Padroni, N. N. Patwardhan, M. Schapira, A. E. Hargrove
RSC MEDICINAL CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Umuhire Aline Juru, Zhengguo Cai, Adina Jan, Amanda E. Hargrove
CHEMICAL COMMUNICATIONS
(2020)