Editorial Material
Oncology
Xuanqi Liu, Diane C. Wang, Charles A. Powell, Xiangdong Wang
Summary: Peripheral immune cells are important for maintaining hemostasis. Single-cell RNA sequencing can be used to measure circulating blood cells, but challenges arise due to the complexity of immune cell development, regulation, and function. Precisely defining cell subset identity is crucial for clinical translation of scRNA-seq.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
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
Biochemistry & Molecular Biology
Nidhi Chauhan, Kirti Saxena, Utkarsh Jain
Summary: Single molecule detection is crucial for understanding the physical and chemical properties as well as mechanisms involved in the normal functioning of body cells. This review highlights various traditional methods and biosensing technologies that offer single molecule sensitivity. The discussion includes plasmonic resonance, nanopores, whispering gallery mode, Simoa assay, recognition tunneling, as well as biosensor-based detection using plasmonic, SERS, CRISPR/Cas, and other types of biosensors. The review provides an overview of the progression in different techniques employed for single molecule detection.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Oncology
Dragomirka Jovic, Xue Liang, Hua Zeng, Lin Lin, Fengping Xu, Yonglun Luo
Summary: Single-cell RNA sequencing technology is an advanced method for studying the diversity and complexity of RNA transcripts within individual cells, and for understanding the composition and functions of different cell types in highly organized tissues/ organs/ organisms. This technology has made significant contributions to various fields, providing unique insights into health and diseases. It can be used to construct high-resolution atlases of cells in all living organisms, and has the potential to transform current protocols in disease diagnosis and treatment.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Review
Genetics & Heredity
Cyrine E. Haidar, Kristine R. Crews, James M. Hoffman, Mary Relling, Kelly E. Caudle
Summary: Pharmacogenomic testing is effective in enhancing medication safety and efficacy. However, preemptive testing poses logistical concerns, such as reimbursement, result reporting, and portability. Lessons can be learned from institutions that have implemented preemptive testing.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
(2022)
Article
Multidisciplinary Sciences
Yanbo Wang, W. Taylor Cottle, Haobo Wang, Momcilo Gavrilov, Roger S. Zou, Minh-Tam Pham, Srinivasan Yegnasubramanian, Scott Bailey, Taekjip Ha
Summary: We describe a method called sgGOLDFISH for direct visualization of point mutations in situ, which can differentiate wild-type and mutant sequences with single-nucleotide sensitivity. This method has potential applications in studying genetic diseases and nuclear biology.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Ilias Papadopoulos, Arjun Menon, Fabian Plass, Desire Molina, Christina Harreiss, Axel Kahnt, Erdmann Spiecker, Angela Sastre-Santos, Dirk M. Guldi
Summary: This study investigates the excited state charge-transfer interactions between SWCNTs and various substituted DPPs, providing insights into their electronic communication mechanism and transfer efficiencies of up to 81% through a range of spectroscopic techniques. Additionally, the successful preparation of stable DPP/SWCNTs as a potential alternative in emerging applications, such as solar energy conversion, is highlighted.
Article
Chemistry, Multidisciplinary
Fan Yang, Ni Ya Li, Ye Ge, Dong Liu
Summary: Irradiation of single crystals of a ladder-like coordination chain with 365 nm UV light induces a regiospecific photochemical [2 + 2] cycloaddition reaction, leading to the formation of a two-dimensional (4,4)-connected coordination network through single-crystal to single-crystal transformation.
Article
Chemistry, Analytical
Ruolan Huang, Kun Liu, Chensirong Yue, Ying Wang, Zhilong Zeng, Lu Xiao, Lei Dong, Rongqin Ke, Chaoyong Yang, Dan Liu
Summary: This study developed a method for visualizing mRNA at single-molecule resolution using rolling circle amplification and streptavidin-modified alkaline phosphatase (SA-ALP) detection. The method provides highly selective and sensitive RNA detection, comparable to fluorescence-based assays. It also overcomes common background interference issues and allows for the quantification of mRNA expression from two genes in single cells and multiple cell types.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Chunlei Liu, Hao Huang, Pengyi Yang
Summary: Multimodal single-cell omics technologies allow for simultaneous profiling of multiple molecular programs in individual cells, providing a new level of resolution for studying biological systems. However, integrating and analyzing multimodal single-cell omics data presents challenges due to the lack of suitable methods. In this study, we propose Matilda, a multi-task learning method that can perform data simulation, dimension reduction, cell type classification, and feature selection in a unified framework. We compare Matilda with other state-of-the-art methods using datasets from popular multimodal single-cell omics technologies, and show its utility in addressing multiple key tasks in integrative analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Qingkang Meng, Yan Zhang, Guoqi Li, Yunong Li, Hongbo Xie, Xiujie Chen
Summary: This study used lncRNAs as typing markers and combined single-cell expression profiles to retype glioblastoma, revealing significant intratumoral heterogeneity and different biological characteristics among subtypes that have varying effects on patient survival. Based on the analysis results, therapeutic drugs were screened for each subtype, and a new precision treatment strategy was proposed.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Review
Genetics & Heredity
Giuseppe Iacomino
Summary: miRNAs are small noncoding RNAs that regulate gene expression at the posttranscriptional level. Dysregulation of miRNAs reflects the state and function of cells and tissues, contributing to their dysfunction. The identification of extracellular miRNAs in biological fluids highlights their potential as biomarkers, while their therapeutic potential is gaining attention. However, challenges such as stability, delivery systems, and bioavailability need to be addressed. Biopharmaceutical companies are increasingly involved in this field, and ongoing clinical trials suggest that anti-miR and miR-mimic molecules may have innovative therapeutic applications. This article provides an overview of pending issues and new opportunities offered by miRNAs in disease treatment and early diagnostics.
Article
Multidisciplinary Sciences
Nico Curti, Giuseppe Levi, Enrico Giampieri, Gastone Castellani, Daniel Remondini
Summary: One of the objectives in high-throughput genomics studies is to obtain a low-dimensional set of observables for sample classification purposes. We propose a network-based heuristic method called DNetPRO to generate feature sets. Applications on real datasets show that our method outperforms existing results or is compatible with them with a smaller number of selected features. Moreover, the resulting class-separation surfaces have a simpler geometry, allowing for clearer interpretation of the obtained features compared to nonlinear classification models.
SCIENTIFIC REPORTS
(2022)
Review
Chemistry, Physical
Yingwen Chen, Jia Song, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong Yang
Summary: Cells are fundamental building blocks of biological systems, and studying single cells can provide insights into cell diversity and disease processes. Single-cell RNA sequencing technologies allow cellular heterogeneity to be dissected at unprecedented resolution.
Review
Cardiac & Cardiovascular Systems
Xinjie Xu, Xiumeng Hua, Han Mo, Shengshou Hu, Jiangping Song
Summary: This review summarizes the application of single-cell RNA sequencing (scRNA-seq) in cardiovascular diseases, revealing the discovery of cardiovascular cellular heterogeneity and potential disease targets, and providing new insights into the promise of scRNA-seq technology in precision medicine and clinical application.
BASIC RESEARCH IN CARDIOLOGY
(2023)
Article
Zoology
Claudia A. Grillo, Mande Holford, Nils G. Walter
Summary: This article proposes using agent-based models to define general rules for interactions across biological systems and evolutionary time, and speculates on the possibility of simulating self-organizing systems and deciphering universal principles that govern biological interactions. It aims to explore further advancements in biosciences in the 21st century.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Rajeev Yadav, Julia R. Widom, Adrien Chauvier, Nils G. Walter
Summary: This study used single molecule fluorescence technology to reveal three dynamically interconverting conformations of the fluoride riboswitch. Specifically, the fluoride ion snap-locks the conformation through its interaction with magnesium-induced RNA, and a long-range base pair plays a crucial role in the process. Additionally, the proximally paused RNA polymerase further promotes riboswitch docking. Finally, the study found that fluoride binding at short RNA lengths is an early step towards folding into the docked conformation.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Zi Li, Molly McNeely, Erin Sandford, Muneesh Tewari, Alexander Johnson-Buck, Nils G. Walter
Summary: From traditional enzyme-linked immunosorbent assay (ELISA) to modern next-generation sequencing, many sensitive and specific biomarker detection assays require capturing analytes at a surface. However, surface-based assays have limited capture efficiency from dilute solutions, resulting in detection sensitivity in the femtomolar-to-nanomolar range. To address this challenge, we use an aqueous two-phase system (ATPS) to concentrate target molecules near the assay surface, improving capture efficiency and achieving subfemtomolar detection limits without amplification. This approach enhances the sensitivity of surface-based assays by approximately 300-fold.
Article
Chemistry, Multidisciplinary
Aaron T. Blanchard, Zi Li, Elizabeth C. Duran, Catherine E. Scull, J. Damon Hoff, Keenan R. Wright, Victor Pan, Nils G. Walter
Summary: DNA-based FluoroCubes were developed as a solution to photobleaching in fluorescence microscopy. These compact FluoroCubes, coupled with up to 6 fluorescent dyes, exhibit enhanced photostability up to 50 times and emit a higher number of photons up to 40 times compared to single dyes. The study addresses the mechanism behind the improved photostability and confirms the compatibility of FluoroCubes with FRET and dark quenching applications.
Article
Biochemistry & Molecular Biology
Sujay Ray, Shiba S. Dandpat, Surajit Chatterjee, Nils G. Walter
Summary: The noncoding, structured 5'-untranslated regions (5'-UTRs) of bacterial mRNAs can regulate translation efficiency through the formation of structures that interact with the ribosome. This study investigates how the binding of a small ligand controls the recruitment and dissociation of the bacterial ribosome to the Shine-Dalgarno sequence. It is found that ligand binding stabilizes the riboswitch structure, which both inhibits ribosome recruitment and accelerates ribosome dissociation. The proximity of the 5'-UTR and the stability of the SD:anti-SD interaction play important roles in modulating the initial ribosome-mRNA interaction.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biophysics
Tanmay Chatterjee, Alexander Johnson-Buck, Nils G. Walter
Summary: Sensitive assays of protein biomarkers play a critical role in clinical diagnostics and biomedical research. Nucleic acid aptamers generated by SELEX have shown promise as an alternative to immunoreagents for detection, offering advantages in synthesis and reproducibility. SiMREPS, a single molecule recognition platform, allows for high sensitivity detection of biomarkers without requiring high-affinity probes. This study demonstrates the applicability of aptamers as detection probes in SiMREPS for two clinically relevant biomarkers, VEGF165 and IL-8, with detection limits in the low femtomolar range.
BIOSENSORS & BIOELECTRONICS
(2022)
Correction
Chemistry, Multidisciplinary
Aaron T. Blanchard, Zi Li, Elizabeth C. Duran, Catherine E. Scull, J. Damon Hoff, Keenan R. Wright, Victor Pan, Nils G. Walter
Article
Biochemistry & Molecular Biology
Adrien Chauvier, Jason C. C. Porta, Indrajit Deb, Emily Ellinger, Katarina Meze, Aaron T. T. Frank, Melanie D. D. Ohi, Nils G. G. Walter
Summary: This study investigates the interaction between RNA polymerase and nascent transcripts during transcription. It is found that the transcription process of a preQ(1) riboswitch can be modulated by the RNA polymerase and the conformation of the nascent RNA. Ligand binding to the riboswitch leads to the release of RNA polymerase pause and the continuation of transcription. The mechanism by which riboswitch folding modulates pausing is revealed through cryo-electron microscopy reconstructions.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Cell Biology
Elizabeth Duran, Andreas Schmidt, Robb Welty, Ameya P. Jalihal, Sethuramasundaram Pitchiaya, Nils G. Walter
Summary: Cellular machineries that drive gene expression and regulate it rely on the assembly and interactions of proteins and RNA called ribonucleoprotein complexes (RNPs). Recreating these cellular machines and understanding their mechanisms is challenging. Single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts can provide insights into the behavior of specific biomolecules within RNPs in native cellular environments. This review discusses the methods and strategies used in dissecting RNP-driven processes, with a focus on pre-mRNA splicing and transcription regulation.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Pharmacology & Pharmacy
Emily Ellinger, Adrien Chauvier, Rosa A. Romero, Yichen Liu, Sujay Ray, Nils G. Walter
Summary: This review examines the potential of riboswitches as novel antibacterial drug targets. The limited mechanisms of action of currently available antibiotics are summarized, followed by a delineation of the functional mechanisms of riboswitches. The potential for developing novel approaches that target paradigmatic riboswitches in the context of their bacterial gene expression machinery is discussed.
EXPERT OPINION ON THERAPEUTIC TARGETS
(2023)
Article
Chemistry, Physical
Guoming Gao, Nils G. Walter
Summary: Biomolecular condensates are membraneless cellular compartments formed by phase separation, which play crucial roles in regulating cellular functions. Live-cell single particle tracking has revealed the mesoscopic organization and biological functions of condensates. However, there is a lack of quantitative benchmarking and objective comparison of boundary detection methods for condensates. In this study, synthetic data with defined ground truth is used to evaluate the most commonly used methods for condensate boundary detection, providing guidance for selecting optimal methods in imaging-based studies of condensates.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Nanoscience & Nanotechnology
Mathias Centola, Erik Poppleton, Sujay Ray, Martin Centola, Robb Welty, Julian Valero, Nils G. Walter, Petr Sulc, Michael Famulok
Summary: Molecular engineering aims to design nanoassemblies for complex tasks, but efficient chemical-fuel-driven nanoscale driver-follower systems have not been realized. In this study, a DNA nanomachine driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates was developed, generating rhythmic pulsating motion and successfully coupling with a passive follower.
NATURE NANOTECHNOLOGY
(2023)
Review
Urology & Nephrology
Guoming Gao, Emily S. Sumrall, Sethuramasundaram Pitchiaya, Markus Bitzer, Simon Alberti, Nils G. Walter
Summary: The regulation of solute microenvironments is crucial for cellular homeostasis. In the kidney, biomolecular condensates formed through hyperosmotic phase separation play important roles in kidney physiology and disease.
NATURE REVIEWS NEPHROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Qian Hou, Surajit Chatterjee, Paul E. Lund, Krishna C. Suddala, Nils G. Walter
Summary: This study investigates the thermodynamic and kinetic folding properties of two riboswitches from different bacteria and the effects of urea and trimethylamine N-oxide (TMAO) on their folding. The results show that the riboswitch from a thermophilic bacterium is more thermotolerant and that urea destabilizes their folded structure while TMAO counteracts urea denaturation. These findings shed light on how subtle sequence adaptations in a thermophilic bacterium can stabilize a common RNA structure.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Rebecca T. Perelman, Andreas Schmidt, Umar Khan, Nils G. Walter
Summary: This study investigates the spatial localization and diffusion of mRNA in cellular ribonucleoprotein (RNP) granules. The results show that mRNA molecules are often localized at the boundaries of these granules, potentially due to intermolecular interactions.