Article
Biotechnology & Applied Microbiology
Sinan Arslan, Francisco J. Garcia, Minghao Guo, Matthew W. Kellinger, Semyon Kruglyak, Jake A. LeVieux, Adeline H. Mah, Haosen Wang, Junhua Zhao, Chunhong Zhou, Andrew Altomare, John Bailey, Matthew B. Byrne, Chiting Chang, Steve X. Chen, Byungrae Cho, Claudia N. Dennler, Vivian T. Dien, Derek Fuller, Ryan Kelley, Omid Khandan, Michael G. Klein, Michael Kim, Bryan R. Lajoie, Bill Lin, Yu Liu, Tyler Lopez, Peter T. Mains, Andrew D. Price, Samantha R. Robertson, Hermes Taylor-Weiner, Ramreddy Tippana, Austin B. Tomaney, Su Zhang, Minna Abtahi, Mark R. Ambroso, Rosita Bajari, Ava M. Bellizzi, Chris B. Benitez, Daniel R. Berard, Lorenzo Berti, Kelly N. Blease, Angela P. Blum, Andrew M. Boddicker, Leo Bondar, Chris Brown, Chris A. Bui, Juan Calleja-Aguirre, Kevin Cappa, Joshua Chan, Victor W. Chang, Katherine Charov, Xiyi Chen, Rodger M. Constandse, Weston Damron, Mariam Dawood, Nicole DeBuono, John D. Dimalanta, Laure Edoli, Keerthana Elango, Nikka Faustino, Chao Feng, Matthew Ferrari, Keith Frankie, Adam Fries, Anne Galloway, Vlad Gavrila, Gregory J. Gemmen, James Ghadiali, Arash Ghorbani, Logan A. Goddard, Adriana Roginski Guetter, Garren L. Hendricks, Jendrik Hentschel, Daniel J. Honigfort, Yun-Ting Hsieh, Yu-Hsien Hwang Fu, Scott K. Im, Chaoyi Jin, Shradha Kabu, Daniel E. Kincade, Shawn Levy, Yu Li, Vincent K. Liang, William H. Light, Jonathan B. Lipsher, Tsung-li Liu, Grace Long, Rui Ma, John M. Mailloux, Kyle A. Mandla, Anyssa R. Martinez, Max Mass, Daniel T. McKean, Michael Meron, Edmund A. Miller, Celyne S. Moh, Rachel K. Moore, Juan Moreno, Jordan M. Neysmith, Cassandra S. Niman, Jesus M. Nunez, Micah T. Ojeda, Sara Espinosa Ortiz, Jenna Owens, Geoffrey Piland, Daniel J. Proctor, Josua B. Purba, Michael Ray, Daisong Rong, Virginia M. Saade, Sanchari Saha, Gustav Santo Tomas, Nicholas Scheidler, Luqmanal H. Sirajudeen, Samantha Snow, Gudrun Stengel, Ryan Stinson, Michael J. Stone, Keoni J. Sundseth, Eileen Thai, Connor J. Thompson, Marco Tjioe, Christy L. Trejo, Greg Trieger, Diane Ni Truong, Ben Tse, Benjamin Voiles, Henry Vuong, Jennifer C. Wong, Chiung-Ting Wu, Hua Yu, Yingxian Yu, Ming Yu, Xi Zhang, Da Zhao, Genhua Zheng, Molly He, Michael Previte
Summary: We introduce avidity sequencing, a sequencing chemistry that optimizes the processes of stepping along a DNA template and identifying each nucleotide separately. By using multivalent nucleotide ligands and dye-labeled cores, nucleotide identification is achieved through polymerase-polymer-nucleotide complexes bound to clonal copies of DNA targets. This approach decreases the required concentration of reporting nucleotides and yields high accuracy.
NATURE BIOTECHNOLOGY
(2023)
Article
Engineering, Environmental
Yu Hu, Zhen Meng, YanZhu Hu, WenJia Tian, YanYing Yang, ShunLi Gao
Summary: This study proposes an improved model of dynamic accident spreading in networks by analyzing complex network theory and STDP mechanism. It explores the interrelationships of elements in work safety accidents and demonstrates the model's effectiveness in simulating the spreading process and edge weight evolution of actual accidents in different types of networks.
PROCESS SAFETY AND ENVIRONMENTAL PROTECTION
(2022)
Article
Multidisciplinary Sciences
E. R. Moody, R. Obexer, F. Nickl, R. Spiess, S. L. Lovelock
Summary: Therapeutic oligonucleotides have become a powerful drug modality for treating diseases, but the increasing number of therapies presents challenges in manufacturing. This study presents a biocatalytic method that can efficiently produce oligonucleotides in a single operation using polymerases and endonucleases to amplify complementary sequences. The method uses unprotected building blocks and aqueous conditions, and demonstrates versatility in synthesizing clinically relevant oligonucleotide sequences with diverse modifications.
Review
Microbiology
Dipika Mishra, Ramanujam Srinivasan
Summary: Partitioning the replicated genetic material into the daughter cells is a crucial process in the cell cycle. Bacteria use cytoskeletal proteins similar to eukaryotic actin and tubulin to segregate plasmids into daughter cells. ParA ATPase interacts with the segregation complex and partitions DNA into daughter cells.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Shijing Yu, Sarah Rempel, Negin Gholamipourbarogh, Christian Beste
Summary: This study reveals the temporally nested representational dynamics during the opening and closing of working memory gates using different EEG analysis methods. It also shows that these dynamics are attributable to a ventral stream-prefrontal cortex processing cascade.
COMMUNICATIONS BIOLOGY
(2022)
Editorial Material
Cell Biology
Argyris Papantonis, Vassilis Roukos
Summary: During DNA repair by homologous recombination, damaged DNA utilizes intact, similar sequences as templates. The study by Piazza, Bordelet and colleagues reveals that cohesin plays a role in restricting homology search during recombination, independent of sister chromatid cohesion.
NATURE CELL BIOLOGY
(2021)
Article
Chemistry, Analytical
Li Guan, Yanyan Zhou, Xiao Li, Yongbao Mao, Anyang Li, Yile Fu, Wen Liu, Sheying Dong, Zhen Liang, Yukui Zhang, Qun Zhao, Lihua Zhang
Summary: A universal strategy has been developed to synthesize pentamethine cyanines with different aromatic heterocycle substituents on the meso-polymethine chain, leading to the development of specific fluorescent probes with high sensitivity and robust OFF/ON switching for targeting G4s. These probes exhibit self-quenching in aqueous solution due to H-aggregation, but can be triggered to emit fluorescence upon recognition of G-quadruplexes.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Yao Wang, Tao Qi, Jingtong Liu, Yuan Yang, Ziwen Wang, Ying Wang, Tianyi Wang, Miaomiao Li, Mingqing Li, Daru Lu, Alex Chia Yu Chang, Li Yang, Song Gao, Yongming Wang, Feng Lan
Summary: The CRISPR-Cas system can treat autosomal dominant diseases by disrupting mutant alleles through nonhomologous end joining (NHEJ). However, current CRISPR-Cas systems cannot differentiate many single-nucleotide mutations from wild-type alleles. We identified Cas12j-8 as an ideal genome editor with comparable activity to AsCas12a and Un1Cas12f1. Cas12j-8 is a highly specific nuclease sensitive to single-nucleotide mismatches in the protospacer adjacent motif (PAM)-proximal region. It enables allele-specific disruption of genes with single-nucleotide polymorphisms (SNPs) and has potential therapeutic applications.
Article
Immunology
Stanislav Dikiy, Jun Li, Lu Bai, Menglin Jiang, Laura Janke, Xinying Zong, Xiaolei Hao, Beatrice Hoyos, Zhong-Min Wang, Beisi Xu, Yiping Fan, Alexander Y. Rudensky, Yongqiang Feng
Summary: The CNS0 enhancer ensures robust Treg cell differentiation early in postnatal life and cooperatively minimizes autoimmunity with other tolerance mechanisms.
Article
Chemistry, Multidisciplinary
Koki Makino, Etsuo A. Susaki, Motomu Endo, Hiroyuki Asanuma, Hiromu Kashida
Summary: This study presents a color-changing fluorescent barcode (CCFB) approach that allows for multiple labeling with a simple nucleic acid structure design. The CCFB method is easy to operate and time-saving, and has been successfully used for labeling multiple targets and detecting intracellular proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biology
Anna Anchimiuk, Virginia S. Lioy, Florian Patrick Bock, Anita Minnen, Frederic Boccard, Stephan Gruber
Summary: SMC complexes are essential for organizing and segregating chromosomes, but the mechanism behind their movement along DNA remains largely unknown. Factors such as loading sites, residency time, translocation rate, and abundance of complexes influence bacterial chromosome organization by modulating the frequency of encounters between SMC complexes. Fine-tuned parameters help to reduce collisions and resolve them effectively.
Article
Chemistry, Multidisciplinary
Ziran Jiang, Aochiu Chen, Jeffrey Chen, Arman Sekhon, Gordon V. Louie, Joseph P. Noel, James J. La Clair, Michael D. Burkart
Summary: This study developed a probe based on the natural product cerulenin for fluorescent labeling and crosslinking to evaluate protein-protein interactions. Additionally, two new masked crosslinking probes were described for activity and structure studies of biosynthetic pathways.
Article
Biochemical Research Methods
Benjamin S. Johnson, Lexie Chafin, Daniela Farkas, Jessica Adair, Ajit Elhance, Laszlo Farkas, Joseph S. Bednash, James D. Londino
Summary: This study modified the structure of BioID2 to create a smaller and more efficient biotin ligase called MicroID2. Compared to other biotin ligases, MicroID2 demonstrated higher labeling activity and lower background labeling. Additionally, a mutant of MicroID2 called lbMi-croID2 was developed for experiments requiring precise temporal control of labeling. Finally, the utility of MicroID2 in mass spectrometry experiments was demonstrated.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Ilaria Rosso, Corey Jones-Weinert, Francesca Rossiello, Matteo Cabrini, Silvia Brambillasca, Leonel Munoz-Sagredo, Zeno Lavagnino, Emanuele Martini, Enzo Tedone, Massimiliano Garre, Julio Aguado, Dario Parazzoli, Marina Mione, Jerry W. Shay, Ciro Mercurio, Fabrizio d'Adda di Fagagna
Summary: This study found that telomeric dilncRNAs are significantly elevated in ALT cells, and inhibition of teloC dilncRNAs leads to DNA replication stress responses, increased genomic instability, and selective induction of apoptosis in ALT cells. These results reveal the essential role of teloC dilncRNA in coordinating the recruitment of DDR factors to ALT telomeres and the survival of ALT cancer cells.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Marcelo Ozu, Juan Jose Alvear-Arias, Miguel Fernandez, Agustin Caviglia, Antonio Pena-Pichicoi, Christian Carrillo, Emerson Carmona, Anselmo Otero-Gonzalez, Jose Antonio Garate, Gabriela Amodeo, Carlos Gonzalez
Summary: AQPs are small transmembrane tetrameric proteins that facilitate water, solute and gas exchange. Their ability to modulate water membrane permeability in response to specific regulators has been experimentally demonstrated. Studies have shown that the repositioning of conserved residues contributes to restricting water permeation in the channel.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Adam S. B. Jalal, Ngat T. Tran, Clare E. Stevenson, Elliot W. Chan, Rebecca Lo, Xiao Tan, Agnes Noy, David M. Lawson, Tung B. K. Le
Article
Evolutionary Biology
Mohak Sharda, Anjana Badrinarayanan, Aswin Sai Narain Seshasayee
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biology
Asha Mary Joseph, Saheli Daw, Ismath Sadhir, Anjana Badrinarayanan
Summary: Translesion synthesis (TLS) is a crucial mutagenic DNA lesion tolerance pathway that utilizes specialized low-fidelity DNA polymerases, such as DnaE2, to synthesize across lesions. In replication-independent conditions, DnaE2 plays a DNA damage-dependent role in facilitating lesion repair, contributing to genome integrity. The interplay between nucleotide excision repair (NER) and specialized polymerases in gap-filling mechanisms helps enhance cell survival and maintain genome integrity in a replication-independent manner.
Article
Biochemistry & Molecular Biology
Adam S. B. Jalal, Ngat T. Tran, Ling J. Wu, Karunakaran Ramakrishnan, Martin Rejzek, Giulia Gobbato, Clare E. M. Stevenson, David M. Lawson, Jeff Errington, Tung B. K. Le
Summary: This study reveals that the nucleoid occlusion protein Noc functions as a CTPase enzyme, with its membrane-binding activity regulated by a CTP switch. It forms large membrane-associated nucleoprotein complexes to physically block assembly of the cell division machinery, providing a new understanding of the mechanisms involved in nucleoid occlusion.
Correction
Multidisciplinary Sciences
Marcin J. Szafran, Tomasz Malecki, Agnieszka Strzalka, Katarzyna Pawlikiewicz, Julia Dulawa, Anna Zarek, Agnieszka Kois-Ostrowska, Kim C. Findlay, Tung B. K. Le, Dagmara Jakimowicz
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Marcin J. Szafran, Tomasz Malecki, Agnieszka Strzalka, Katarzyna Pawlikiewicz, Julia Dulawa, Anna Zarek, Agnieszka Kois-Ostrowska, Kim C. Findlay, Tung B. K. Le, Dagmara Jakimowicz
Summary: Bacteria of the genus Streptomyces have a linear chromosome and undergo substantial rearrangement during sporulation, transitioning from an 'open' to a 'closed' conformation, similar to eukaryotes.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Nitish Dua, Akshaya Seshadri, Anjana Badrinarayanan
Summary: Mitochondria are essential organelles involved in cell growth and survival. Recent research has shown that maintaining the distribution and organization of mitochondria is crucial for maintaining the stability of the mitochondrial genome. However, the impact of DNA damage on mitochondrial dynamics and the loss of mtDNA is not well understood. This study developed a tool to induce mitochondria-specific DNA damage and observed dynamic reorganization of mitochondrial networks and mtDNA loss. Surprisingly, perturbation to the exonuclease function of mtDNA replicative polymerase also resulted in rapid mtDNA loss. The findings highlight the importance of genome maintenance for mitochondrial function and organelle organization.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Afroze Chimthanawala, Jyotsana J. Parmar, Sujan Kumar, Krishnan S. Iyer, Madan Rao, Anjana Badrinarayanan
Summary: This study uncovers three key elements of homology search driven by RecN: the mobility of a finite segment of RecA, dynamic changes in filament length, and the ability to conduct multiple pole-to-pole traversals.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Aditya Kamat, Anjana Badrinarayanan
Summary: Cells have specialized pathways to sense and respond to DNA damage, with bacteria having the well-studied SOS response and other SOS-independent DNA damage responses. The diversity in response and repair mechanisms raises important questions about their influence on genomes and vice versa. This review discusses recent insights on three SOS-independent bacterial DNA damage responses, exploring the mysteries of their diversity generation and regulation in cells for genome integrity maintenance.
CURRENT OPINION IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kirill V. Sukhoverkov, Adam S. B. Jalal, James R. Ault, Frank Sobott, David M. Lawson, Tung B. K. Le
Summary: In Bacillus subtilis, a ParB-like protein called Noc binds specifically to Noc-binding sites (NBSs) on the chromosome to coordinate chromosome segregation and cell division. Noc forms large membrane-associated nucleoprotein complexes by binding to CTP, which physically inhibits the assembly of the cell division machinery. The structure of Noc bound to NBS DNA reveals important conformational changes that occur during the binding process.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Asha Mary Joseph, Kazi Nahar, Saheli Daw, Md. Mahbub Hasan, Rebecca Lo, Tung B. K. Le, Khondaker Miraz Rahman, Anjana Badrinarayanan
Summary: Pyrrolobenzodiazepines (PBDs) are DNA binding compounds with anti-tumor and anti-bacterial activity. Chemical modifications can enhance their DNA binding and efficacy. Our study shows that PBD monomers cause DNA damage and kill bacteria, and repairing these damages rely on error-free mechanisms.
RSC MEDICINAL CHEMISTRY
(2022)