Review
Neurosciences
Anaelle Aurelie Dumas, Katharina Borst, Marco Prinz
Summary: Microglial cells play diverse roles in the CNS and new systems for analyzing them are becoming more specific and complex. Single-cell technologies and transgenic mouse models have been crucial in studying microglia, but there are clear limitations. Understanding the advantages and pitfalls of these tools is essential for their proper application.
Article
Biochemistry & Molecular Biology
Zhixin Lei, Haowei Meng, Yuan Zhuang, Qingguo Zhu, Chengqi Yi
Summary: This article outlines the off-target effects observed for various genome editing tools and discusses the methods for detecting and evaluating off-target editing, along with their advantages and limitations. Additionally, it summarizes current RNA editing tools for RNA therapy and medicine that can potentially serve as alternative approaches to genome editing tools in research and clinical applications.
ACS CHEMICAL BIOLOGY
(2023)
Review
Immunology
Abhijit Saha, Alberto Fernandez-Tejada
Summary: O-GlcNAc glycosylation is an important post-translational modification in mammalian cells, regulated by two enzymes. Aberrant expression of O-GlcNAc has been implicated in diseases such as Alzheimer's, diabetes, and cancer, and recent research has shown its key implications in immunity. However, the mechanistic understanding of O-GlcNAcylated proteins in the immune system is still limited due to difficulties in mapping and quantifying O-GlcNAc sites. This mini-review discusses recent progress in chemical biology tools and approaches to investigate the role of O-GlcNAcylation in immune cells, aiming to inspire further research and developments in glycoimmunology.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Microbiology
Alexandra L. Krause, Timothy P. Stinear, Ian R. Monk
Summary: This review highlights the lag in molecular biology research on Enterococcus faecalis and Enterococcus faecium compared to other Gram-positive pathogens and discusses methods to overcome barriers in DNA transfer. Improving transformation techniques will expedite our understanding of these important pathogens.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Sport Sciences
Daniel T. Cervone, Roger Moreno-Justicia, Julia Prats Quesada, Atul S. Deshmukh
Summary: Recent studies have found that both acute exercise and chronic exercise training have positive effects on the entire body's physiology, which are mainly attributed to significant changes in tissue-specific proteins. Particularly, skeletal muscle, as the major contributor to exercise, has attracted the attention of exercise scientists who aim to uncover adaptive mechanisms resulting in metabolic benefits and performance enhancements from training. With the emergence of mass spectrometry-based proteomics, researchers are now able to study muscle protein dynamics comprehensively from various perspectives. This review highlights recent literature that employs new workflows and advancements in proteomics to deepen our understanding of training-related changes in skeletal muscle. The authors also emphasize the need to explore untapped areas in skeletal muscle proteomics research and address key considerations when applying mass spectrometry-based analyses, especially in the study of human biology. They further encourage researchers to combine omics data with functional analyses to enhance our knowledge of the complex adaptive responses in skeletal muscle during acute and chronic exercise.
SCANDINAVIAN JOURNAL OF MEDICINE & SCIENCE IN SPORTS
(2023)
Review
Developmental Biology
Steffen Wolf, Yinan Wan, Katie McDole
Summary: Advances in light microscopy, labelling strategies and computational methods have enabled detailed investigations into cell fates, and when combined with genomics and single-cell transcriptomics, developmental biology can describe embryo formation in unprecedented detail. The review discusses different strategies and applications for lineage tracing in live-imaging data, as well as outlining software methodologies for various cell-tracking challenges.
Article
Biochemical Research Methods
Joseph H. R. Hetmanski, Matthew C. Jones, Fatima Chunara, Jean-Marc Schwartz, Patrick T. Caswell
Summary: Cell migration in 3D environments relies on the coordinated activity of leading edge protrusion and rear retraction in a push-pull mechanism. This study used three different mathematical modelling approaches to investigate the signalling dynamics of rapid rear retraction, deriving new insights into cell rear dynamics and uncovering a novel role for CDK1 in driving cell rear movement. Our multi-faceted approach highlighted the importance of integrating different modelling techniques to gain a comprehensive understanding of complex biological systems.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Daniel Braatz, Mariam Cherri, Michael Tully, Mathias Dimde, Guoxin Ma, Ehsan Mohammadifar, Felix Reisbeck, Vahid Ahmadi, Michael Schirner, Rainer Haag
Summary: Poor water solubility and low bioavailability of active pharmaceutical ingredients (APIs) are major challenges in pharmaceutical drug development. Drug delivery remains a key challenge for both small-molecule drugs and biopharmaceuticals. This Review provides insights into the challenges and requirements for designing and translating new polymer-based delivery systems, with a focus on chemical approaches for systemic drug delivery.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemical Research Methods
Corrado Priami
Summary: Computational methods are increasingly important in elucidating biological systems, with this paper reviewing the most useful technologies in nutrient metabolism and metabolic disorders. While specific examples are not explored in detail due to space constraints, pointers to relevant papers are provided.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Diego Perez-Dones, Mario Ledesma-Terron, David G. Miguez
Summary: The study of vertebrate retina development can be approached from various perspectives, ranging from qualitative to quantitative, and focuses on spatial-temporal features, three-dimensional structure, and regulation at the systems level. Using the example of the developing zebrafish retina, the importance of image quality, processing, and algorithms in extracting quantitative data from dense three-dimensional tissues is highlighted. It is suggested that the scientific community focusing on developmental systems could greatly benefit from a detailed disclosure of tools and pipelines used for processing and analyzing images from biological samples.
Review
Biochemistry & Molecular Biology
Vesper Burjoski, Anireddy S. N. Reddy
Summary: RNAs transmit information from DNA to encode proteins and regulate gene expression. Recent studies have uncovered a hidden landscape of RNA-protein interactions in plants. Application of modern techniques has led to the discovery of close to 2000 putative RNA-binding proteins in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Jeffrey A. Dewey, Cleimence Delalande, Saara-Anne Azizi, Vivian Lu, Dionysios Antonopoulos, Gyorgy Babnigg
Summary: This article reviews the identification methods and strategies of small-molecule molecular glues and introduces the classification of currently approved glues. The importance of factors such as experimental conditions, software packages, and genetic tools is highlighted, and the curation of this method hopes to inspire diverse research efforts targeting a multitude of human diseases.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Review
Oncology
Ali Zarrabi, David Perrin, Mahboubeh Kavoosi, Micah Sommer, Serap Sezen, Parvaneh Mehrbod, Bhavya Bhushan, Filip Machaj, Jakub Rosik, Philip Kawalec, Saba Afifi, Seyed Mohammadreza Bolandi, Peiman Koleini, Mohsen Taheri, Tayyebeh Madrakian, Marek J. Los, Benjamin Lindsey, Nilufer Cakir, Atefeh Zarepour, Kiavash Hushmandi, Ali Fallah, Bahattin Koc, Arezoo Khosravi, Mazaher Ahmadi, Susan Logue, Gorka Orive, Stevan Pecic, Joseph W. Gordon, Saeid Ghavami
Summary: Rhabdomyosarcoma is a rare cancer that affects skeletal muscle, primarily in children and young adults. The treatment strategies for this disease include multi-agent chemotherapies following surgical resection and radiotherapy. This review provides a detailed clinical understanding of rhabdomyosarcoma, including its classification, diagnosis, and treatment strategies. The impact of apoptosis, macro-autophagy, and the unfolded protein response on chemotherapy response is discussed. Additionally, the use of in vivo mouse and zebrafish models and in vitro three-dimensional bioengineering models for screening future therapeutic approaches and promoting muscle regeneration is explored.
Article
Multidisciplinary Sciences
Yuri Frosi, Yen-Chu Lin, Jiang Shimin, Siti Radhiah Ramlan, Kelly Hew, Alf Henrik Engman, Anil Pillai, Kit Yeung, Yue Xiang Cheng, Tobias Cornvik, Par Nordlund, Megan Goh, Dilraj Lama, Zachary P. Gates, Chandra S. Verma, Dawn Thean, David P. Lane, Ignacio Asial, Christopher J. Brown
Summary: An attractive approach to target intracellular macromolecular interfaces and model putative drug interactions is to design small high-affinity proteins. Here, the authors engineer and optimize an autonomous and disulfide-free human VH domain for intracellular expression, and identify several VH domain binders against eIF4E, a protein commonly hyper-activated in cancer. These VH domains interact with eIF4E at the eIF4G binding site via a distinct structural pose, and their intracellular overexpression reduces cellular proliferation and expression of malignancy-related proteins in cancer cell lines. The linkage of high-diversity in vitro libraries with an intracellularly expressible miniprotein scaffold facilitates the discovery of VH domains suitable for intracellular applications.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Garrison A. Nickel, Katharine L. Diehl
Summary: This review examines the development of methods for characterizing proteins that interact with histone and DNA modifications. Mark first and reader first approaches are complementary strategies that greatly enhance our understanding of chromatin modifications in genomic regulation.
ACS CHEMICAL BIOLOGY
(2023)
