Article
Biotechnology & Applied Microbiology
Ke Liu, Gui-Hong Lin, Kun Liu, Yong-Jun Liu, Xin-Yi Tao, Bei Gao, Ming Zhao, Dong-Zhi Wei, Feng-Qing Wang
Summary: In this study, a multiplexed integrase-assisted site-specific recombination (miSSR) method was developed to integrate genes/pathways in Mycolicibacteria for the purpose of constructing cell factories. The method successfully integrated multiple copies of genes using different bacteriophage systems and a reconstructed Xer recombinase system. The results showed that the miSSR system is an effective and convenient tool for engineering the genomes of Mycolicibacteria and other related strains.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Microbiology
Lauren A. Riley, Irenee C. Payne, Melissa Tumen-Velasquez, Adam M. Guss
Summary: This study developed a system for integrating up to 12 genetic constructs into the E. coli chromosome. Site-specific recombinases were used to catalyze recombination between specific DNA sequences, enabling the integration of heterologous DNA. The utility of this system was demonstrated by the insertion of eight DNA methyltransferases into the E. coli chromosome.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Microbiology
Jing Yang, Lina Liu, Yu Feng, Da He, Chengcheng Wang, Zhiyong Zong
Summary: The newly identified mcr-10 plasmid-borne colistin resistance gene was found in a Cronobacter sakazakii isolate. It may be mobilized through site-specific recombination mediated by an integrase of an integrative mobile element.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Microbiology
Gang Zhang, Qinna Cui, Jianjuan Li, Ruiliang Guo, Sebastien Olivier Leclercq, Lifeng Du, Na Tang, Yuqin Song, Chao Wang, Fangqing Zhao, Jie Feng
Summary: In this study, the mobility of GIsul2 and CR2-sul2 units mediated by integrase was experimentally characterized. The results demonstrate that the integrase of GIsul2 can perform the excision and integration of GIsul2 and CR2-sul2 unit by site-specific recombination between att core sites. The findings suggest a potential and unappreciated role of the GIsul2 integrase family in the dissemination of CR2-sul2 units carrying various resistance determinants.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Vishnu Hosur, Benjamin E. Low, Michael V. Wiles
Summary: The inability to efficiently and precisely insert large DNA constructs into the genome is a major challenge in genomic engineering. Existing methods lack precision or have limited capacity. However, a new toolkit combining RNA-guided Cas9 and site-specific integrase Bxb1 has been developed, enabling the integration of DNA constructs ranging from 5 to 43 kb in mouse zygotes and human cells.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Nir Hananya, Sara K. Daley, John D. Bagert, Tom W. Muir
Summary: The study developed a efficient semi-synthesis method to create full-length ADP-ribosylated histones H3 and H2B, which were used to investigate the roles of histone ADP-ribosylation in DNA damage response. The results showed that ADP-ribosylation of serine-6 of histone H2B inhibits chromatin folding and higher-order organization, providing new insights into the impact of histone modifications on chromatin structure.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Kimihiro Abe, Takumi Takahashi, Tsutomu Sato
Summary: This study demonstrates the importance of the extreme C-terminal region (ECT) of SprA in DNA recombination and directionality control in Bacillus subtilis. The interaction between SprA and SprB is influenced by the alanine residue Phe532 in the extreme C-terminal region, affecting the directional control of the recombination reaction.
MOLECULAR MICROBIOLOGY
(2021)
Article
Engineering, Electrical & Electronic
Jingyan Ma, Jie Liu, Yupeng Tian, Guangmin Sun, Kai Zhang, Yu Li
Summary: In this article, a Ku-band high directivity antenna is designed and its radiation performance is improved by optimizing the structural parameters. The calculation method between key technical indexes and structural parameters is established, and finite-element analysis and COMSOL simulation software are used for study.
IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION
(2022)
Article
Multidisciplinary Sciences
Brydon Eastman, Michelle Przedborski, Mohammad Kohandel
Summary: The study shows that chemotherapeutic dosing strategies learned through reinforcement learning methods are more resilient to perturbations in patient-specific parameter values. By training an agent on mean-value parameters and allowing periodic access to a more easily measurable metric, relative bone marrow density, drug dosing schedules that outperform classical optimal control methods can be developed.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Joshua R. Elmore, Gara N. Dexter, Henri Baldino, Jay D. Huenemann, Ryan Francis, V. George L. Peabody, Jessica Martinez-Baird, Lauren A. Riley, Tuesday Simmons, Devin Coleman-Derr, Adam M. Guss, Robert G. Egbert
Summary: SAGE is a highly efficient and extensible genome engineering technology that allows selection marker-free, site-specific genome integration of multiple DNA constructs in bacteria. It shows superior efficiency compared to replicating plasmids and overcomes host range limitations. SAGE has the potential to expand high-throughput genetics and synthetic biology in industrial and environmental bacteria.
Review
Biochemistry & Molecular Biology
Irina O. Petrova, Svetlana A. Smirnikhina
Summary: Prime editing is a CRISPR/Cas-based genome editing method. This review discusses its mechanism, optimization strategies, and future developments. The components of a prime editing system, including a prime editor fusion protein and prime editing guide RNA, have been optimized for improved efficiency. The recruitment of mismatch repair inhibitors and the combination of prime editors with integrases are potential next steps for further advancements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Gang Zhang, Shigang Yao, Yunan Liu, Hailing Fang, Yuqin Song, Chao Wang, Dawei Wei, Jie Feng
Summary: In this study, we identified 530 novel tyrosine-type integrases from bacterial genomic islands. These integrases belong to a distinct evolutionary clade and are affiliated with new integrase groups. The integration functions of six representative novel integrases were validated in a bacterial model system, and their expression patterns were confirmed in Escherichia coli. This study revealed site-specific recombination functions of novel integrases and expands the toolbox for genetic engineering.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Nafiseh Sanei Ata-Abadi, Mahboobeh Forouzanfar, Kianoush Dormiani, Shiva Rouhollahi Varnosfaderani, Leila Pirjamali, Mohammad Hossein Nasr-Esfahani, Reza Moradi Hajidavaloo
Summary: In this study, we successfully constructed stable cell lines in HEK293T cells using the PhiC31 integrase system, which can efficiently produce and secrete active rhPH20. Quantitative and functional analysis showed that the secreted rhPH20 had specific activity and could remove cumulus cells from oocytes. Additionally, the results demonstrated the ability of the PhiC31 enzyme to insert the PH20-expressing donors into specific pseudo attP sites in the genome of target cells with different copy numbers.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Hematology
Andrea Calabria, Carlo Cipriani, Giulio Spinozzi, Laura Rudilosso, Simona Esposito, Fabrizio Benedicenti, Alessandra Albertini, Marie Pouzolles, Mirko Luoni, Serena Giannelli, Vania Broccoli, Mickael Guilbaud, Oumeya Adjali, Naomi Taylor, Valerie S. Zimmermann, Eugenio Montini, Daniela Cesana
Summary: Adeno-associated virus (AAV) vectors have been successfully used in gene therapy for genetic disorders. AAV can integrate into the host cell genome, and our study found that in T cells, AAV integrations mainly occur within the T-cell receptor genes. This finding suggests new possibilities for long-term AAV-mediated gene transfer in dividing cells.
Article
Biochemistry & Molecular Biology
Yun-Hsiu Tseng, Tien-Li Ma, Dun-Heng Tan, An-Jey A. Su, Kia M. Washington, Chun-Chieh Wang, Yu-Ching Huang, Ming-Chung Wu, Wei-Fang Su
Summary: This study reports the development of an anisotropic structured hydrogel scaffold created by co-injection of cellulose nanofiber (CNF) solution and co-polypeptide solution. The hydrogel is mechanically strong and able to support, guide, and stimulate neurite growth. Based on the experimental results, the researchers conclude that this novel material and unique injection method have a high potential for application in neural tissue engineering.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Femi J. Olorunniji, Arlene L. McPherson, Hania J. Pavlou, Michael J. McIlwraith, John A. Brazier, Richard Cosstick, W. Marshall Stark
NUCLEIC ACIDS RESEARCH
(2015)
Article
Biotechnology & Applied Microbiology
Paul C. M. Fogg, Joshua A. Haley, W. Marshall Stark, Margaret C. M. Smith
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2017)
Review
Biochemistry & Molecular Biology
Femi J. Olorunniji, Susan J. Rosser, W. Marshall Stark
BIOCHEMICAL JOURNAL
(2016)
Article
Biochemistry & Molecular Biology
Alexandra Pokhilko, Jia Zhao, Oliver Ebenhoeh, Margaret C. M. Smith, W. Marshall Stark, Sean D. Colloms
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biology
Aleksandra Bebel, Ezgi Karaca, Banushree Kumar, W. Marshall Stark, Orsolya Barabas
Editorial Material
Biochemistry & Molecular Biology
W. Marshall Stark
MOLECULAR MICROBIOLOGY
(2011)
Article
Biochemistry & Molecular Biology
Marko M. Prorocic, Dong Wenlong, Femi J. Olorunniji, Aram Akopian, Jan-Gero Schloetel, Adele Hannigan, Arlene L. McPherson, W. Marshall Stark
NUCLEIC ACIDS RESEARCH
(2011)
Article
Biochemistry & Molecular Biology
Sean D. Colloms, Christine A. Merrick, Femi J. Olorunniji, W. Marshall Stark, Margaret C. M. Smith, Anne Osbourn, Jay D. Keasling, Susan J. Rosser
NUCLEIC ACIDS RESEARCH
(2014)
Article
Multidisciplinary Sciences
Chris Proudfoot, Arlene L. McPherson, Andreas F. Kolb, W. Marshall Stark
Article
Multidisciplinary Sciences
Femi J. Olorunniji, Dorothy E. Buck, Sean D. Colloms, Andrew R. McEwan, Margaret C. M. Smith, W. Marshall Stark, Susan J. Rosser
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Biochemistry & Molecular Biology
Ross A. Keenholtz, Sally-J. Rowland, Martin R. Boocock, W. Marshall Stark, Phoebe A. Rice
Article
Biochemistry & Molecular Biology
Sally-J Rowland, Martin R. Boocock, Mary E. Burke, Phoebe A. Rice, W. Marshall Stark
MOLECULAR MICROBIOLOGY
(2020)
Article
Biochemical Research Methods
Nidda F. Waraich, Shruti Jain, Sean D. Colloms, William Marshall Stark, Nicolas P. Burton, Anthony Maxwell
Article
Microbiology
W. Marshall Stark
MICROBIOLOGY SPECTRUM
(2014)