Article
Agricultural Engineering
Yan-Yu Chen, Yuki Soma, Masahito Ishikawa, Masatomo Takahashi, Yoshihiro Izumi, Takeshi Bamba, Katsutoshi Hori
Summary: This study compared the metabolic alterations of Methylococcus capsulatus (Bath) in gas-phase reactions and aqueous phase reactions, showing significant changes in cell metabolism in the gas-phase reaction. The findings suggest that cells adjust their metabolism to adapt to different substrate conditions, which could facilitate the development of low-energy methane-based bioproduction processes.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yi-Fang Tsai, Thiyagarajan Natarajan, Zhi-Han Lin, I-Kuen Tsai, Damodar Janmanchi, Sunney I. Chan, Steve S. -F. Yu
Summary: This study presents a strategy for the electrocatalysis of selective methane oxidation by immobilizing tricopper catalysts on the cathodic surface. The technology achieves significant enhancements in performance of the catalysts toward methane oxidation, leading to high product throughputs and turnover frequencies. It is of great importance for the on-site direct conversion of methane into methanol.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Biochemistry & Molecular Biology
Si-Wei Wang, Chao Gao, Yi-Min Zheng, Li Yi, Jia-Cheng Lu, Xiao-Yong Huang, Jia-Bin Cai, Peng-Fei Zhang, Yue-Hong Cui, Ai-Wu Ke
Summary: The CRISPR/Cas9 gene editing technology has made significant progress in oncological research, providing a powerful tool for exploring the mechanism of cancer, establishing tumor models, and studying drug targets.
Review
Materials Science, Multidisciplinary
Shao Wei Hu, Tao Ding, Honghai Tang, Huiping Guo, Wenguo Cui, Yilai Shu
Summary: With the advancement of genome editing techniques, gene therapy is increasingly being used for the treatment of various human diseases. Nanomaterials have shown great potential in improving the efficiency and safety of gene editing in gene therapy. This review introduces three gene editing tools, with a particular focus on the development and optimization of the CRISPR system. It also discusses the recent application of nanobiomaterials in gene therapy, along with the prospects and remaining challenges. Lastly, future directions for gene editing tools, nanobiomaterial vectors, and gene therapy are presented.
Article
Biology
Ganna Reint, Zhuokun Li, Kornel Labun, Salla Keskitalo, Inkeri Soppa, Katariina Mamia, Eero Tolo, Monika Szymanska, Leonardo A. Meza-Zepeda, Susanne Lorenz, Artur Cieslar-Pobuda, Xian Hu, Diana L. Bordin, Judith Staerk, Eivind Valen, Bernhard Schmierer, Markku Varjosalo, Jussi Taipale, Emma Haapaniemi
Summary: Precision CRISPR gene editing can be improved by fusing DNA repair proteins with Cas9, with different fusion proteins showing varying effects based on cell type and genomic site. Optimization is necessary to account for the diverse factors contributing to locus-specific genome editing outcomes.
Review
Biotechnology & Applied Microbiology
Congting Guo, Xiaoteng Ma, Fei Gao, Yuxuan Guo
Summary: Gene editing involves precise changes to specific nucleic acid sequences. The CRISPR/Cas9 system has revolutionized gene editing, making it efficient, convenient, and programmable. However, off-target effects remain a major concern, leading to unexpected alterations in the genome. Various methods have been developed to detect and mitigate these off-target effects, advancing the precision of CRISPR/Cas9 derivatives. This review summarizes these technological advancements and discusses the challenges in managing off-target effects for future gene therapy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Man-han Yu, Xue-shan Li, Jia Wang, Matt Longshaw, Kai Song, Ling Wang, Chun-xiao Zhang, Kang-le Lu
Summary: This study aimed to evaluate the effects of substituting fish meal with methanotroph bacteria meal on the growth performance, non-specific immunity and gut health of Lateolabrax maculatus. The results showed that replacing 30% fish meal with 14% methanotroph bacteria meal did not have a negative effect on the growth performance of spotted seabass, while substituting 3.5% methanotroph bacteria meal enhanced the growth and immune function of the fish. Additionally, substituting 20-30% fish meal with 7-10.5% methanotroph bacteria meal increased the abundance of beneficial bacteria in the fish intestine.
ANIMAL FEED SCIENCE AND TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
J. Boutin, J. Rosier, D. Cappellen, F. Prat, J. Toutain, P. Pennamen, J. Bouron, C. Rooryck, J. P. Merlio, I. Lamrissi-Garcia, G. Cullot, S. Amintas, V. Guyonnet-Duperat, C. Ged, J. M. Blouin, E. Richard, S. Dabernat, F. Moreau-Gaudry, A. Bedel
Summary: The study reveals the genotoxicity caused by CRISPR-Cas9 leading to loss of heterozygosity changes, while also highlighting the potential safety concerns of this technology for gene therapy.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Hidehiro Ito, Kosei Yoshimori, Masahito Ishikawa, Katsutoshi Hori, Toshiaki Kamachi
Summary: In this study, a methanol production system was established using methanotroph mutants to control the expression of methanol dehydrogenase (MDH), allowing for methanol accumulation. By modulating the metal ion composition, the conditions for cell growth inhibition and methanol accumulation were repeatedly alternated, showcasing the potential for efficient conversion of methane to methanol.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Jin Chang, Peng Peng, Muhammad Farhan Ul-Haque, Abid Hira, Alan A. DiSpirito, Jeremy D. Semrau
Summary: Copper plays a critical role in controlling greenhouse gas emissions, and methanobactin (MB) secreted by methanotrophs can limit the ability of other microbes to gather copper, thereby impacting microbial community composition. This study shows that different forms of MB increased nitrous oxide (N2O) production and caused significant shifts in microbial community composition in forest soils. The effects of MB were strongest in low-copper soils, and MB-SB2 had a stronger effect due to its higher affinity for copper. The presence of MB also inhibited nitrite reduction and altered the presence of specific genes involved in denitrification.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Plant Sciences
Guo-Qing Song, Grace Urban, John T. Ryner, Gan-Yuan Zhong
Summary: This study evaluated chimeric editing in gene editing, using a transgenic tobacco line and a CRISPR-Cas9 editing vector. It was found that chimeric editing primarily occurred during or after cell regeneration. Further transformation was conducted to enhance editing efficiency. The findings provide valuable information for understanding gene editing in plant cells using constitutively expressed CRISPR-Cas9 and gRNAs.
Review
Cell Biology
Heba M. Mansour, Aiman S. El-Khatib
Summary: This article reviews the pathogenesis of Parkinson's disease (PD) and its association with CRISPR/Cas9 gene editing technology. It introduces the kinases encoding genes related to PD and targeted control by CRISPR/Cas9 technology. It also discusses the off-target effects of the CRISPR/Cas9 system and how to address them, as well as the challenges and future directions in kinase research for PD.
AGEING RESEARCH REVIEWS
(2023)
Article
Ecology
Christina S. Kang-Yun, Xujun Liang, Philip Dershwitz, Wenyu Gu, Aloys Schepers, Andrew Flatley, Josef Lichtmannegger, Hans Zischka, Lijie Zhang, Xia Lu, Baohua Gu, Joshua C. Ledesma, Daly J. Pelger, Alan A. DiSpirito, Jeremy D. Semrau
Summary: Aerobic methanotrophy is strongly regulated by copper, with different methanotrophs utilizing various mechanisms for copper uptake, including secreting methanobactin or utilizing proteins like MopE. Certain methanotrophs are able to steal methanobactin from others, enhancing their ability to degrade methylmercury. Understanding these strategies may help manipulate methanotrophic communities to reduce methane emissions and enhance mercury detoxification.
Article
Biochemical Research Methods
Stefan J. Tekel, Nicholas Brookhouser, Kylie Standage-Beier, Xiao Wang, David A. Brafman
Summary: The introduction of transient reporters of editing enrichment (TREE) has enabled highly efficient single-base editing of human cells using a transient episomal fluorescent reporter, allowing for rapid generation of clonal editing efficiencies exceeding 80% in biallelic or multiplexed edited isogenic human pluripotent stem cell lines within approximately 3-4 weeks.
Review
Biochemistry & Molecular Biology
Chin-Kai Chuang, Wei-Ming Lin
Summary: Cas9-sgRNA is a key tool for genome editing, with its simplicity, unique RNA-guided DNA recognition activity, and independent nuclease activities. Different variants of Cas9, in combination with sgRNA, can achieve various effects on target site breakage. Additionally, engineered enzyme activities can be introduced using Cas9 derivatives, and methods for transient expression and biosafety have been developed to address off-target effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Fang Qian, Cheng Zhu, Jennifer M. Knipe, Samantha Ruelas, Joshuah K. Stolaroff, Joshua R. DeOtte, Eric B. Duoss, Christopher M. Spadaccini, Calvin A. Henard, Michael T. Guarnieri, Sarah E. Baker
Article
Microbiology
Cristal Zuniga, Chien-Ting Li, Geng Yu, Mahmoud M. Al-Bassam, Tingting Li, Liqun Jiang, Livia S. Zaramela, Michael Guarnieri, Michael J. Betenbaugh, Karsten Zengler
NATURE MICROBIOLOGY
(2019)
Correction
Microbiology
Cristal Zuniga, Chien-Ting Li, Geng Yu, Mahmoud M. Al-Bassam, Tingting Li, Liqun Jiang, Livia S. Zaramela, Michael Guarnieri, Michael J. Betenbaugh, Karsten Zengler
NATURE MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Qiang Fei, Bobo Liang, Ling Tao, Eric C. D. Tan, Ramon Gonzalez, Calvin A. Henard, Michael T. Guarnieri
BIOCHEMICAL ENGINEERING JOURNAL
(2020)
Article
Multidisciplinary Sciences
Cristal Zuniga, Tingting Li, Michael T. Guarnieri, Jackson P. Jenkins, Chien-Ting Li, Kerem Bingol, Young-Mo Kim, Michael J. Betenbaugh, Karsten Zengler
NATURE COMMUNICATIONS
(2020)
Review
Energy & Fuels
Jeffrey G. Linger, Leah R. Ford, Kavita Ramnath, Michael T. Guarnieri
FRONTIERS IN ENERGY RESEARCH
(2020)
Article
Biology
Sara Calhoun, Tisza Ann Szeremy Bell, Lukas R. Dahlin, Yuliya Kunde, Kurt LaButti, Katherine B. Louie, Andrea Kuftin, Daniel Treen, David Dilworth, Sirma Mihaltcheva, Christopher Daum, Benjamin P. Bowen, Trent R. Northen, Michael T. Guarnieri, Shawn R. Starkenburg, Igor V. Grigoriev
Summary: Researchers characterized the growth and biomass accumulation of a halotolerant microalga Scenedesmus sp. NREL 46B-D3 using functional genomics, showing peak growth at 25 degrees C with high biomass accumulation capacity. Functional genomics analysis revealed changes in lipid metabolism and amino acid synthesis under temperature stress, providing insight into the genes involved in the metabolic and regulatory response to temperature stress.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lukas R. Dahlin, Michael T. Guarnieri
Summary: This study established a novel photosynthetic protein production platform in the industrial microalga Picochlorum renovo through computational prediction and genetic engineering, successfully achieving functional secretion of the fluorescent protein mCherry. Further characterization showed efficient production of transgenic protein in the culture supernatant.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Review
Biochemical Research Methods
Kathleen L. Arnolds, Lukas R. Dahlin, Lin Ding, Chao Wu, Jianping Yu, Wei Xiong, Cristal Zuniga, Yo Suzuki, Karsten Zengler, Jeffrey G. Linger, Michael T. Guarnieri
Summary: Genetically modified organisms (GMOs) play a vital role in sustainable bioeconomy, but their rapid development raises concerns about biosecurity. Further research is needed to understand the interaction between microbes and biocontainment constraints for maximizing the potential of biocatalytic platforms in the bioeconomy.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Junneng Wen, Kent Rapp, Lukas R. Dahlin, Chien-Ting Li, Jacob Sebesta, Amanda N. Barry, Michael T. Guarnieri, Christie Peebles, Michael Betenbaugh
Summary: Algal technology holds great potential as a source of renewable biomass and bioproducts, but also faces significant challenges. The recent workshop aimed to bring together thought leaders to identify key challenges and propose research strategies to overcome these barriers in algae engineering and cultivation. Themes such as genetic engineering, metabolomics, algal ecology, and data analytics emerged from the discussion.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Biotechnology & Applied Microbiology
Lukas R. Dahlin, Michael T. Guarnieri
Summary: Microalgae, specifically the Picochlorum genus, offer a potential solution for combating climate change by capturing and reducing CO2 to sustainable fuels and chemicals. In this study, the researchers aimed to expand the genetic toolbox available for the Picochlorum genus by heterologously expressing the phosphite dehydrogenase gene. The results showed that the transgenic algae were able to utilize phosphite as a sole phosphorus source and exhibited comparable growth and composition to conventionally grown algae. This research presents new possibilities for genetic engineering and crop protection strategies.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Review
Plant Sciences
Jacob Sebesta, Wei Xiong, Michael T. Guarnieri, Jianping Yu
Summary: Genetically engineered algae can convert light and carbon dioxide into industrially and commercially relevant chemicals. However, there is a need to address the potential risks of releasing these engineered algae into the natural environment, and develop effective biocontainment strategies.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Davinia Salvachua, Patrick O. Saboe, Robert S. Nelson, Christine Singer, Ian McNamara, Carlos del Cerro, Yat-Chen Chou, Ali Mohagheghi, Darren J. Peterson, Stefan Haugen, Nicholas S. Cleveland, Hanna R. Monroe, Michael T. Guarnieri, Eric C. D. Tan, Gregg T. Beckham, Eric M. Karp, Jeffrey G. Linger
Summary: Research on producing butyric acid from lignocellulosic biomass to prepare renewable diesel and jet fuels through Clostridium tyrobutyricum catalysis, with advanced HED-ISPR process reducing overall costs and environmental impact, thus enhancing the viability of renewable fuel production.
CELL REPORTS PHYSICAL SCIENCE
(2021)
Review
Chemistry, Multidisciplinary
R. Gary Grim, Zhe Huang, Michael T. Guarnieri, Jack R. Ferrell, Ling Tao, Joshua A. Schaidle
ENERGY & ENVIRONMENTAL SCIENCE
(2020)