Article
Biochemistry & Molecular Biology
Naomichi Takemata, Stephen D. Bell
Summary: Chromosome conformation capture technologies have identified topologically associating domains and A/B compartments as key features of eukaryotic chromosomes, with Sulfolobus archaea chromosomes also showing unique characteristics. The study reveals local rules governing the organization of topological domains and provides insights into the evolution of eukaryotic chromosome conformation through analysis of prokaryotic chromosome structures.
Review
Biochemistry & Molecular Biology
Alia dos Santos, Christopher P. Toseland
Summary: The nucleus in eukaryotic cells houses the cell's genomic material. Factors like chromatin structure and the nuclear lamina play essential roles in the mechanical properties of the nucleus. Nuclear stiffness impacts and is impacted by cellular processes such as DNA damage and repair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Shengjian Yuan, Juan Shi, Jianrong Jiang, Yingfei Ma
Summary: The CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach was used to reduce the genomes of four distinct phages, resulting in heterogeneous genome-reduced mutants. Loss of non-essential genes for phage propagation was identified, although it had detrimental effects on phage fitness. However, some mutants showed higher infectious efficiency than their parental strains, indicating a trade-off between genome reduction and infectious fitness for phages. This study provides a foundation for future phage synthetic biology research leveraging CiPGr.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Hannes Becher, Jacob Sampson, Alex D. Twyford
Summary: Genome size variation within plant taxa is caused by presence/absence variation, which affects low-copy sequences or genomic repeats of different frequency classes. In this study, a novel approach based on k-mers is used to analyze genome size variation in diploid eyebrights. The results show that the sequences underlying genome size variation are mainly rDNA sequences, a genomic satellite, and a repeat associated with an Angela transposable element. This study also emphasizes the importance of studying non-repetitive sequences to fully understand genome size variation.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Chemistry, Multidisciplinary
Ana Valente, Luis Vieira, Maria Joao Silva, Celia Ventura
Summary: DNA methylation is an epigenetic mechanism that involves the addition of a methyl group to a cytosine residue in CpG dinucleotides, which are particularly abundant in gene promoter regions. Studies have shown that modifications of DNA methylation may have an impact on the adverse health effects caused by exposure to environmental toxicants. This review aims to investigate the possible impact of nanomaterials on DNA methylation.
Article
Biochemical Research Methods
Todor Gitchev, Gabriel Zala, Peter Meister, Daniel Jost
Summary: Recent studies have found that the loop extrusion activity of Structural Maintenance of Chromosomes complexes plays a central role in genome organization. Polymer physics-based modeling allows researchers to assess the structures that this extrusion can create and compare them with experimental data. However, only a few labs have the technical and computational expertise to create these simulation models.
Review
Biotechnology & Applied Microbiology
Li-Fu Song, Zheng-Hua Deng, Zi-Yi Gong, Lu-Lu Li, Bing-Zhi Li
Summary: Significant progress has been made in large-scale de novo oligonucleotide synthesis based on phosphoramidite chemistry in recent decades, with a focus on applications such as de novo genome synthesis and DNA data storage. However, challenges remain in improving synthesis length, speed, cost, and throughput, which can be addressed by utilizing enzymatic methods. This review summarizes the current status of large-scale oligonucleotide synthesis technologies and discusses opportunities and challenges in de novo genome synthesis and DNA data storage.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Elizabeth L. Clare, Chloe K. Economou, Frances J. Bennett, Caitlin E. Dyer, Katherine Adams, Benjamin McRobie, Rosie Drinkwater, Joanne E. Littlefair
Summary: The study demonstrates that DNA from terrestrial animals can be extracted from air samples and used to identify species and their ecological interactions. This method has significant potential for monitoring terrestrial ecosystems.
Article
Optics
Aaron Z. Goldberg, Guillaume S. Thekkadath, Khabat Heshami
Summary: Coherence is fundamental to quantum phenomena and plays a role in classical theories as well, but understanding its significance can be challenging. The quadrature coherence scale (QCS) was developed to precisely quantify quantum features in a single-mode bosonic system without bias towards any specific phase space orientation. The QCS can be calculated for any state and reduces to well-known quantities in certain limits, making it a valuable tool for measuring coherence. Recent progress has allowed for the measurement of QCS in squeezed light and thermal states using Xanadu's machine Borealis, which offers the necessary components for precise measurements. The results confirm the utility of interferometers and photon-counting devices in verifying quantum properties.
Article
Physics, Multidisciplinary
R. A. Dumer, M. Godoy
Summary: The nonequilibrium Ising model on a restricted scale-free network has been studied using Monte Carlo simulations. The dynamics of the system are defined by the probability of one- and two-spin flip processes, simulating contact with a heat bath or an external flux of energy. The study found finite critical points and calculated thermodynamic quantities and critical exponents for the system.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2023)
Article
Genetics & Heredity
Meili Chen, Yingke Ma, Song Wu, Xinchang Zheng, Hongen Kang, Jian Sang, Xingjian Xu, Lili Hao, Zhaohua Li, Zheng Gong, Jingfa Xiao, Zhang Zhang, Wenming Zhao, Yiming Bao
Summary: The Genome Warehouse (GWH) is a public repository that houses genome assembly data for various species and offers web services for data submission, storage, release, and sharing. With a uniform quality control procedure, GWH accepts full and partial genome sequences and visualizes released data using JBrowse, serving as an important resource for global research activities.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Tatsuya Yoneji, Hironobu Fujita, Takahito Mukai, Masayuki Su'etsugu
Summary: This study developed a method to split the genome-reduced E. coli into three 1 Mb chromosomes, which allows for further genetic engineering of tripartite-genome cells with minimal impact on growth rate. Additionally, the purified 1 Mb chromosomes can be successfully electroporated into other cells under experimental conditions.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Business
Volker G. Kuppelwieser, Phil Klaus
Summary: This study systematically explored the psychometric properties of the EXQ scale and found that it comprises two or more dimensions, challenging the previous conceptualization. The research also explores the relationships between these dimensions and takes a step toward generalizing the new EXQ scale, advancing our understanding of the role that CX quality plays in different research settings.
JOURNAL OF BUSINESS RESEARCH
(2021)
Article
Polymer Science
Aishuang Liu, Yanbo Yao, Jingwen Yao, Tao Liu
Summary: This study unifies droplet spreading and film wrinkling to propose a new dynamic wrinkling phenomenon. Through experiments and theoretical formulations, it is shown that this method provides insights into wrinkling behavior and offers a convenient way to measure the elastic moduli of thin films.
Article
Biotechnology & Applied Microbiology
Jan Burian, Vincent K. Libis, Yozen A. Hernandez, Liliana Guerrero-Porras, Melinda A. Ternei, Sean F. Brady
Summary: The capture of metagenomic DNA in large clone libraries allows for the study of microbial diversity that cannot be accessed using culture-dependent methods. In this study, a CRISPR counter-selection interruption circuit (CCIC) using nuclease-deficient Cas9 was developed to retrieve target clones from complex libraries. Combining modern sequencing methods with CCIC cloning enables rapid access to the genetic diversity present in natural ecosystems. A CRISPRi method was used to retrieve sequences of interest from large metagenomic libraries.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Simon Veth, Adrian Fuchs, Dilara Oezdemir, Clemens Dialer, David Jan Drexler, Fabian Knechtel, Gregor Witte, Karl-Peter Hopfner, Thomas Carell, Evelyn Ploetz
Summary: The cGAS-STING pathway plays a crucial role in sensing cytosolic DNA. Research on the development of fluorescent moieties and synthesis of fluorescent molecules for detection is important for the therapeutic potential of this pathway.
Review
Biochemistry & Molecular Biology
Taekjip Ha, Christian Kaiser, Sua Myong, Bin Wu, Jie Xiao
Summary: Due to their unique abilities to manipulate, label, and image individual molecules, single-molecule techniques provide unprecedented access to elementary biological processes.
Article
Biochemistry & Molecular Biology
Felix J. Metzner, Elisabeth Huber, Karl-Peter Hopfner, Katja Lammens
Summary: The Schlafen family, including SLFN5, plays important roles in cell cycle regulation, DNA repair, etc. The structure of SLFN5 differs from ATPase and can bind both tRNA and DNA, possibly involved in transcriptional regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Shuyi Zhang, Jacob R. Leistico, Raymond J. Cho, Jeffrey B. Cheng, Jun S. Song
Summary: This study introduces two spectral algorithms on multilayer graphs for clustering cells in multi-omic single-cell sequencing datasets, demonstrating the WLL method as a new spectral graph theoretic reformulation of the popular Seurat weighted nearest neighbor algorithm.
Article
Chemistry, Multidisciplinary
Hossein Moghimianavval, Chintan Patel, Sonisilpa Mohapatra, Sung-Won Hwang, Tunc Kayikcioglu, Yashar Bashirzadeh, Allen P. Liu, Taekjip Ha
Summary: InterSpy is introduced as a synthetic biology tool for engineering membrane-membrane interfaces. It allows tracking and reconstitution of functional fluorescent protein between apposing synthetic or cell membranes, demonstrating the potential for designing non-native cellular communication pathways and creating synthetic tissues. The technology is tested using a mammalian cell-free expression system and shows promising results.
Article
Chemistry, Multidisciplinary
Samuele Stazzoni, Daniel F. R. Bohmer, Fabian Hernichel, Dilara Oezdemir, Aikaterini Pappa, David Drexler, Stefan Bauernfried, Gregor Witte, Mirko Wagner, Simon Veth, Karl-Peter Hopfner, Veit Hornung, Lars M. Koenig, Thomas Carell
Summary: 2',3'-cGAMP is a second messenger formed during cellular recognition of foreign cytosolic DNA, binding to the adaptor protein STING to induce an immune response. Studies show that analogs lacking secondary ribose-OH groups can serve as poxin-resistant STING agonists, with dideoxy-2',3'-cAAMP showing high antitumor response in mice.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biology
Claudia C. Carcamo, Matthew F. Poyton, Anand Ranjan, Giho Park, Robert K. Louder, Xinyu A. Feng, Jee Min Kim, Thuc Dzu, Carl Wu, Taekjip Ha
Summary: This study characterizes the 1D scanning properties of SWR1, a chromatin remodeler, and reveals the impacts of various factors on its scanning process. By directly observing SWR1 diffusion on DNA, the study demonstrates that ATP and a DNA-binding subunit play important roles in the overall diffusive behavior of the complex. The findings provide valuable insights into the role of SWR1 in chromatin remodeling.
Article
Immunology
Nina Kessler, Susanne F. Viehmann, Calvin Krollmann, Karola Mai, Katharina M. Kirschner, Hella Luksch, Prasanti Kotagiri, Alexander M. C. Boehner, Dennis Huugen, Carina C. de Oliveira Mann, Simon Otten, Stefanie A. Weiss, Thomas Zillinger, Kristiyana Dobrikova, Dieter E. Jenne, Rayk Behrendt, Andrea Ablasser, Eva Bartok, Gunther Hartmann, Karl-Peter Hopfner, Paul A. Lyons, Peter Boor, Angela Roesen-Wolff, Lino L. Teichmann, Peter Heeringa, Christian Kurts, Natalio Garbi
Summary: The study identifies abnormal DNA recognition and IFN-I production as drivers of severe ANCA-associated vasculitis, and demonstrates that blocking this pathway can ameliorate the disease and accelerate recovery, suggesting potential therapeutic targets for patients.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Cell Biology
Roger S. Zou, Alberto Marin-Gonzalez, Yang Liu, Hans B. Liu, Leo Shen, Rachel K. Dveirin, Jay X. J. Luo, Reza Kalhor, Taekjip Ha
Summary: Here, we propose an approach that combines CRISPR system with high-throughput sequencing to target hundreds of epigenetically diverse endogenous genomic sites simultaneously, measuring Cas9 dynamics and cellular responses. The use of multi-target guide RNAs (mgRNAs) enables massive multiplexing of CRISPR, providing insights into Cas9 binding, cleavage, and cellular response to DNA damage.
NATURE CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Momcilo Gavrilov, Joshua Y. C. Yang, Roger S. Zou, Wen Ma, Chun-Ying Lee, Sonisilpa Mohapatra, Jimin Kang, Ting-Wei Liao, Sua Myong, Taekjip Ha
Summary: Polymerase Chain Reaction (PCR) is a crucial method in molecular diagnostics and life sciences. This study introduces a new method, SHARP (SSB-Helicase Assisted Rapid PCR), which uses an engineered helicase and single-stranded DNA binding protein (SSB) to replace the heating step of PCR. The new method allows the isothermal amplification of DNA fragments up to 6000 base pairs.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Ikenna C. Okafor, Taekjip Ha
Summary: CRISPR Cas9 is an RNA-guided endonuclease that is a part of bacterial adaptive immune system. By developing a single molecule FRET assay, the study investigated the conformational changes of sgRNA and the binding of Cas9 to sgRNA, providing insights into the assembly dynamics of Cas9 RNA ribonucleoprotein complex. This research could contribute to the rational design of sgRNAs and improve the editing outcomes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Aakash Basu, Dmitriy G. Bobrovnikov, Basilio Cieza, Juan Pablo Arcon, Zan Qureshi, Modesto Orozco, Taekjip Ha
Summary: In this study, we comprehensively characterized the mechanical code of DNA using high-throughput experimental methods and developed a physical model to describe the sequence and methylation dependence of DNA deformation. Our measurements and model validations demonstrated that sequence and epigenetic modifications can encode regulatory information in diverse contexts.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Karl-Peter Hopfner
Summary: The Mre11-Rad50-(Nbs1/Xrs2) complex is a conserved factor that repairs DNA double-strand breaks and other DNA termini in all species. It functions as a complex DNA-associated molecular machine that cuts various types of free and obstructed DNA termini for repair, while leaving undamaged DNA intact. Recent studies have revealed the mechanisms of DNA end recognition, endo/exonuclease activities, nuclease regulation, and DNA scaffolding in the Mre11-Rad50 orthologs. This review summarizes our current understanding and recent progress on the functional architecture of Mre11-Rad50 and how it acts as a DNA topology-specific endo/exonuclease.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Biochemistry & Molecular Biology
Stephan Woike, Sebastian Eustermann, James Jung, Simon Josef Wenzl, Goetz Hagemann, Joseph Bartho, Katja Lammens, Agata Butryn, Franz Herzog, Karl-Peter Hopfner
Summary: The Swi2/Snf2 family transcription regulator Mot1 utilizes ATP to remove the TBP from promoters and reposition it on DNA. Cryo-EM structures reveal that Mot1 dissociates TBP without tracking DNA grooves, instead gripping DNA in the presence of ATP and moving TBP to a less stable position. The displaced TBP is then trapped by a chaperone element. Mechanistic similarities are observed with RNA gripping helicases and immune sensors.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aman Y. Husbands, Antje Feller, Vasudha Aggarwal, Courtney E. Dresden, Ashton S. Holub, Taekjip Ha, Marja C. P. Timmermans
Summary: The START domain of the HD-ZIPIII transcription factors plays a crucial role in promoting homodimerization and increasing transcriptional potency, while also binding to phospholipids. This discovery resolves a long-standing mystery in plant development and highlights the regulatory potential of this evolutionary module.