Review
Biochemical Research Methods
Sarah Taeuber, Alexander Gruenberger
Summary: Performance losses commonly occur during the scaling-up of bioprocesses, caused by concentration gradients in bioreactors. Scale-down bioreactors are used to analyze large-scale conditions and predict the successful transfer of bioprocesses from lab to industry. Microfluidic single-cell cultivation (MSCC) systems provide the opportunity to understand cellular processes at a single-cell level. However, current MSCC systems have limited cultivation parameters that do not represent bioprocess-relevant environmental conditions.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Ruobing Guan, Dongdong Chu, Xinyi Han, Xuexia Miao, Haichao Li
Summary: RNA interference (RNAi) technology is widely used in medicine and agriculture, requiring large amounts of low-cost dsRNA. However, current microbial cell-based synthesis of dsRNA has low efficiency and yield, highlighting the need for the development of more efficient microbial dsRNA production systems in the future.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Engineering, Biomedical
Mark C. Allenby, Maria A. Woodruff
Summary: Industrial cell culture processes are expensive, time-consuming, and variable. Recent advances in biomedical image analysis and computational modeling provide opportunities to enhance the design and operation of tissue biomanufacturing platforms, improving efficiency and consistency. This review outlines current resources and approaches that utilize biomedical imaging and image-based computational models for efficient and robust human tissue biomanufacturing.
Editorial Material
Multidisciplinary Sciences
Felicia Kuperwaser, Itai Yanai
Summary: A comprehensive cell atlas of gene expression and regulation in human embryos has provided a unique opportunity for innovative investigation of development through multi-organ and multi-modal analysis.
Article
Biochemical Research Methods
Hannes Russmayer, Markus Buchetics, Matthias Mattanovich, Stefan Neubauer, Matthias Steiger, Alexandra B. Graf, Gunda Koellensperger, Stephan Hann, Michael Sauer, Brigitte Gasser, Diethard Mattanovich
Summary: This study investigated the impact of engineering amino acid metabolism on the production of recombinant proteins. Overexpression of genes related to amino acid metabolism increased intracellular amino acid levels and improved recombinant protein production. The results showed that overexpression of pathway genes and the regulator GCN4 can significantly enhance the production of recombinant proteins.
BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Ryusaku Matsumoto, Yutaka Takahashi
Summary: The pituitary gland plays a crucial role in maintaining systemic homeostasis by secreting hormones, and its development is regulated by the expression of transcription and growth factors. Understanding of the developmental processes and mechanisms of human pituitary disorders is limited due to the lack of a human pituitary developmental model. Recently, methods for inducing pituitary glands from human pluripotent stem cells have been developed, providing new avenues for regenerative medicine and pituitary research.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Beyza Karacaoglu, Benan Inan, Didem Balkanli Ozcimen
Summary: The commercialization of high value-added bioactive compounds from microalgae faces various challenges, such as controlling parameters for process optimization and high production costs. Microfluidic devices are increasingly used in microalgal bioprocess studies due to their unique features, including small scale, controlled parameters, and high throughput capabilities. These devices outperform conventional techniques in terms of functions and analysis of small samples. This review discusses the diverse microfluidic platforms for microalgal processes, including cultivation, purification, separation, sorting, and high-throughput screening.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
Article
Agricultural Engineering
Adriano Gennari, Renate Simon, Bruna Coelho de Andrade, Luis Fernando Saraiva Macedo Timmers, Vera Lucia Milani Martins, Gaby Renard, Jocelei Maria Chies, Giandra Volpato, Claucia Fernanda Volken de Souza
Summary: This study successfully produced and characterized a recombinant Kluyveromyces sp. beta-galactosidase fused to a cellulose-binding domain (CBD) for potential industrial applications. Expression assays and bioreactor scale cultures demonstrated optimal production conditions and results, highlighting the potential for sustainable industrial processes using low-cost inputs.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemical Research Methods
Marje Kasari, Villu Kasari, Mirjam Karmas, Arvi Joers
Summary: This study describes a novel growth switch based on the permanent removal of the origin of replication (oriC) from the Escherichia coli chromosome. Switched cells, which lack oriC, can maintain metabolic activity and protein synthesis capacity even after growth cessation, leading to higher protein levels compared to nonswitching cells. This switcher technology has the potential for wide application in decoupling growth and production in various bacterial species.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Madhavi Perera, Jinyong Yan, Li Xu, Min Yang, Yunjun Yan
Summary: In recent years, vegetable oils and their derivatives have gained attention as environmentally friendly lubricants due to their biodegradability, renewable nature, and superior lubrication performance compared to fossil commercial lubricants. This review examines the zero-waste approach of enzymatic conversion for bio-lubricant production using non-edible oil and agro-industrial waste, while also exploring the use of lipase as a biocatalyst in place of chemically mediated transesterification processes. The article provides information on the types of lipases used, their optimal reaction conditions, and the maximum product yields, as well as highlights the physicochemical properties and enhanced application fields of bio-lubricants.
JOURNAL OF CLEANER PRODUCTION
(2022)
Review
Oncology
Beste Turanli, Ozlem Altay, Jan Boren, Hasan Turkez, Jens Nielsen, Mathias Uhlen, Kazim Yalcin Arga, Adil Mardinoglu
Summary: Drug repositioning is a powerful method that repurposes existing drugs for treatment of diseases. Advances in high-throughput screenings and computational biology have paved the way for rational drug repositioning methods. This approach offers new treatment options for cancer patients.
SEMINARS IN CANCER BIOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Ali Sohrabi Shoabjareh, Fatollah Farhadi, Mahmoud Reza Pishvaie
Summary: This study proposes a new method for simulating bio-processes by integrating conventional simulation softwares such as ASPEN PLUS and MATLAB. The framework utilizes ASPEN PLUS to simulate process equipment and MATLAB to model the bio-reactor using Dynamic Flux Balance Analysis (DFBA) concept. This approach provides a rigorous basic model for both upstream and downstream equipment and can be utilized for process optimization and modern control strategies.
COMPUTERS & CHEMICAL ENGINEERING
(2023)
Review
Environmental Sciences
Deepak Kumar, Raveena Bhardwaj, Sunena Jassal, Tanya Goyal, Aastha Khullar, Naveen Gupta
Summary: This article highlights the significance of different enzymes used in the textile industry at various stages, as well as the advantages of enzymatic approaches, including their eco-friendliness, production of high-quality products, and reduction in energy, water, and time consumption.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemical Research Methods
Kate E. Dray, Joseph J. Muldoon, Niall M. Mangan, Neda Bagheri, Joshua N. Leonard
Summary: Mathematical modeling is crucial for understanding and designing synthetic biological systems. However, the model development process is complex and nonintuitive, requiring iteration and comparison with experimental data. To address these challenges, we introduce the GAMES workflow, which combines automated and human-in-the-loop processes. This workflow enables biologists to more easily build and analyze models for various applications.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Nanoscience & Nanotechnology
Kai Tang, Jianmin Xue, Yufang Zhu, Chengtie Wu
Summary: This review highlights the applications of bioinspired nanomaterials in the biomedical field, focusing on three strategies inspired by natural structures, biomolecules, and bioprocesses. The design concepts, synthesis approaches, and specific roles of various bioinspired nanomaterials in biomedical applications are summarized and discussed. The challenges for the development of bioinspired biomedical nanomaterials, such as mechanical failure in wet environments, limitations in scale-up fabrication, and lack of deep understanding of biological properties, are also addressed. It is expected that interdisciplinary cooperation will further promote the development and clinical translation of bioinspired biomedical nanomaterials.
WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY
(2023)
Editorial Material
Microbiology
Yeah-Ji Ahn, Jong An Lee, Kyeong Rok Choi, Junho Bang, Sang Yup Lee
Summary: This article introduces the advantages of microbe-based carbon capture, sequestration, and utilization (CCSU) technologies over physicochemical and plant-based methods, and describes the role of microorganisms in the global carbon cycle. Strategies to enhance microbe performance and the use of microbes in addressing environmental crises are provided. Finally, the challenges and future prospects of microbe-based CCSU technologies are discussed.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Woo Dae Jang, Gi Bae Kim, Sang Yup Lee
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jong An Lee, Jung Ho Ahn, Gi Bae Kim, Sol Choi, Ji Yeon Kim, Sang Yup Lee
Summary: Mannheimia succiniciproducens, a rumen bacterium, was engineered to produce a high yield of malic acid through pathway reconstruction, respiration system reconstruction, and cell membrane engineering. The strategies used in this study for systems metabolic engineering could be valuable for developing anaerobic bioprocesses for the production of various industrially important chemicals.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Review
Chemistry, Multidisciplinary
Eujin Hong, Junhyeok Jeon, Hyun Uk Kim
Summary: Polypharmacy has become a concern due to the growing elderly population and the emergence of unexpected infections like COVID-19 pandemic. Machine learning models that predict drug-drug interactions (DDIs) have been actively developed to address the challenges of experimentally examining the pharmacological effects of polypharmacy. This review discusses the development of DDI-predicting machine learning models since 2018, including dataset sources, featurization approaches, and types of DDI prediction outcomes.
KOREAN JOURNAL OF CHEMICAL ENGINEERING
(2023)
Review
Biotechnology & Applied Microbiology
Gi Bae Kim, So Young Choi, In Jin Cho, Da-Hee Ahn, Sang Yup Lee
Summary: Bio-based production of chemicals and materials has gained attention for its role in establishing sustainability and improving human health. Metabolic engineering (ME) allows deliberate modification of cellular metabolic, regulatory, and signaling networks to enhance chemical production and degrade harmful substances. Over the past 30 years, ME has advanced significantly through the integration of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. This review provides an overview of the field, highlighting its contributions to sustainable production, health, and the environment through representative examples. Future challenges and perspectives are also discussed.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Baodong Hu, Haibo Yu, Jingwen Zhou, Jianghua Li, Jian Chen, Guocheng Du, Sang Yup Lee, Xinrui Zhao
Summary: By exploiting versatile P450 enzymes, whole-cell biocatalysis can be performed to synthesize valuable compounds in Escherichia coli. However, the insufficient supply of heme limits the whole-cell P450 biocatalytic activity. This study reports a strategy for improving intracellular heme biosynthesis to enhance the catalytic efficiencies of P450s. The strategy involves optimizing intracellular heme biosynthesis through the integrated expression of necessary synthetic genes and the fine-tuning of heme levels using mutated biosensors and regulatory RNA systems.
Article
Chemistry, Multidisciplinary
Ji Yeon Kim, Yeah-Ji Ahn, Jong An Lee, Sang Yup Lee
Summary: Due to the climate crisis and environmental problems caused by reliance on fossil resources, many efforts have been made to establish biorefinery platforms for the bio-based production of chemicals. Systems metabolic engineering has enabled efficient engineering of microorganisms to produce platform chemicals. This paper reviews recent advances and future prospects in the bio-based production of representative platform chemicals, accompanied by a table summarizing their titer, yield, and productivity.
CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY
(2023)
Article
Biochemical Research Methods
Hannah Chung, Jiyong Kim, Yong Jae Lee, Kyeong Rok Choi, Ki Jun Jeong, Geun-Joong Kim, Sang Yup Lee
Summary: A strategy to enhance mRNA stability and improve recombinant protein production in E. coli was developed by knocking down the expression level of RnpA. This strategy successfully allowed the overexpression of 23 different recombinant proteins, including difficult-to-produce proteins, such as Cas9 protein and spider silk protein. This study has broad application potential for the production of recombinant proteins.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Zi Wei Luo, Kyeong Rok Choi, Sang Yup Lee
Summary: This article presents the metabolic engineering of Pseudomonas putida KT2440 strain to convert p-xylene to terephthalic acid through enzymatic catalysis. By integrating heterologous genes into the strain's chromosome and optimizing the fermentation process, a high-yield TPA production was achieved.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Peichao Zhang, Jing Gao, Haiyang Zhang, Yongzhen Wang, Zhen Liu, Sang Yup Lee, Xiangzhao Mao
Summary: Metabolically engineered Escherichia coli strains capable of producing Zosteric acid (ZA) from glucose and glycerol were developed. This was achieved by enhancing the availability of the sulfur donor 3'-phosphoadenosine-5'-phospho-sulfate (PAPS), relieving the feedback regulation of L-tyrosine biosynthesis, deleting competing pathway genes, optimizing carbon source, and other measures. The best-performing strain produced 1.52 g L-1 ZA and 1.30 g L-1 p-hydroxycinnamic acid in a fed-batch bioreactor.
METABOLIC ENGINEERING
(2023)
Article
Chemistry, Analytical
Younseong Song, Seongjin Lim, Yong Tae Kim, Yoo Min Park, Da Ae Jo, Nam Ho Bae, Seok Jae Lee, Bong Gill Choi, Sung Gap Im, Hyun Uk Kim, Kyoung G. Lee
Summary: Accurate analysis of dPCR images is crucial for miniaturizing dPCR system for point-of-care testing. In this study, a deep learning model combined with circle Hough transform was used to perform semantic segmentation and count droplets in low-quality dPCR images. The modified deep learning model achieved rapid, absolute quantification and accurate identification of target DNA, similar to the commercial dPCR system. The deep learning-based approach also demonstrated high sensitivity for detecting pathogenic bacteria from low-quality images. These findings lay the groundwork for efficient nucleic acid quantification and establishment of a point-of-care analysis platform.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Multidisciplinary Sciences
Jae Sung Cho, Dongsoo Yang, Cindy Pricilia Surya Prabowo, Mohammad Rifqi Ghiffary, Taehee Han, Kyeong Rok Choi, Cheon Woo Moon, Hengrui Zhou, Jae Yong Ryu, Hyun Uk Kim, Sang Yup Lee
Summary: Researchers have developed a synthetic sRNA platform that can be used in a wide range of bacteria, allowing knockdown of target genes and reducing virulence-associated phenotypes in pathogens. It can also be used for metabolic engineering to produce specific chemicals. The platform has been successfully tested in 16 bacterial species.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Taehee Han, Sang Yup Lee
Summary: The biosynthesis of Valerolactam (VL) was achieved by metabolically engineered Corynebacterium glutamicum, which overproduces L-lysine. This provides a green and sustainable method for the production of precursor chemicals for nylon-5 and nylon 6,5.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Gahyeon Ryu, Gi Bae Kim, Taeho Yu, Sang Yup Lee
Summary: The establishment of a bio-based circular economy is crucial for addressing the climate crisis and promoting sustainable development. Designing metabolic pathways for microbial cell factories is essential, and computer-supported tools and deep learning techniques can aid in pathway prediction and enzyme discovery. Leveraging these computational tools and strategies, particularly the capabilities of deep learning, has the potential to accelerate the advent of a bio-based circular economy.
METABOLIC ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Won Jun Kim, Youngjoon Lee, Hyun Uk Kim, Jae Yong Ryu, Jung Eun Yang, Sang Yup Lee
Summary: In metabolic engineering, predicting gene overexpression targets is challenging. The iBridge method identifies positive and negative metabolites that impact product formation and identifies bridgereactions as overexpression and downregulation targets. It can be used to optimize the production of numerous chemicals.
