Article
Biotechnology & Applied Microbiology
Ioscani Jimenez del Val, Sarantos Kyriakopoulos, Simone Albrecht, Henning Stockmann, Pauline M. M. Rudd, Karen M. M. Polizzi, Cleo Kontoravdi
Summary: Metabolic modeling is important for characterizing biopharmaceutical cell culture processes. However, current metabolic models of CHO cells face challenges in terms of size and interpretation. To address these challenges, the CHOmpact model was developed as a reduced metabolic network with improved interpretability and physiological consistency. This model provides a platform for developing dynamic metabolic models to optimize biopharmaceutical cell culture processes.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Hyeonjin Cha, Ju-Hyun Park
Summary: The addition of 30Kc19 alpha protein was found to enhance the production of EPO in CHO cell culture, with potential advantages in downstream purification process. 30Kc19 alpha could be mass-produced as a recombinant protein and delivered intracellularly to improve EPO production through metabolic pathways. The results suggest that 30Kc19 alpha has promising potential for manufacturing biopharmaceutical proteins.
APPLIED SCIENCES-BASEL
(2021)
Article
Biology
R. Alan Harris, Muthuswamy Raveendran, Dustin T. Lyfoung, Fritz J. Sedlazeck, Medhat Mahmoud, Trent M. Prall, Julie A. Karl, Harshavardhan Doddapaneni, Qingchang Meng, Yi Han, Donna Muzny, Roger W. Wiseman, David H. O'Connor, Jeffrey Rogers
Summary: By utilizing Oxford Nanopore Technologies long-read sequencing, an improved assembly of the Syrian hamster (M. auratus) genome (BCM_Maur_2.0) was produced, resulting in a chromosome-scale assembly with a total length of 2.46 Gb. The new assembly, BCM_Maur_2.0, exhibits significantly enhanced continuity with a scaffold N50 that is 6.7 times greater than that of MesAur1.0, and it annotates 21,616 protein-coding genes and 10,459 noncoding genes as opposed to 20,495 protein-coding genes and 4,168 noncoding genes in MesAur1.0.
Article
Biochemical Research Methods
Madolyn L. MacDonald, Kelvin H. Lee
Summary: EvalDNA is a tool that utilizes supervised machine learning to score the quality of genome assemblies without the need for a reference genome. It has been successfully applied in various studies for evaluating human and bacterial assemblies, providing scientists with an easy way to identify the best genome assembly for their organism of interest.
BMC BIOINFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Michael A. MacDonald, Matthias Nobel, Dinora Roche Recinos, Veronica S. Martinez, Benjamin L. Schulz, Christopher B. Howard, Kym Baker, Evan Shave, Yih Yean Lee, Esteban Marcellin, Stephen Mahler, Lars Keld Nielsen, Trent Munro
Summary: Over the past 30 years, the biopharmaceutical industry's success has been largely dependent on products derived from Chinese Hamster Ovary (CHO) cell lines, with perfusion processes playing a key role in improving mammalian cell cultures for large-scale fed-batch processes. Recent interest has been regained in perfusion-based bioprocess research, driven by high volumetric titers and a small footprint, especially during the recent pandemic. The future of perfusion bioprocesses looks promising, with emerging trends in media optimization, continuous processing, and cell line engineering holding the greatest potential.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Alina Rekena, Dora Livkisa, Edmunds Kamolins, Juris Vanags, Dagnija Loca
Summary: This study addressed the ongoing discussion about the genotoxic effect of magnetic field (MF) exposure on mammalian cell cultures by developing a simple and cost-effective experimental setup that generated a static MF. Results showed that a 0.66-T static MF exposure had no significant long-term effect on cell viability and chromosomal damage but demonstrated a short-term effect on cell apoptosis, with an increase in nuclear bud formation observed. These findings may inspire future research on cellular responses to MF exposure and provide relevant data for comparison.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Mauro Torres, Hirra Hussain, Alan J. Dickson
Summary: This review highlights the importance of mammalian cell factories, particularly the CHO cell system, in biopharmaceutical production. It provides an overview of the secretory pathway, the challenges in protein production, and the advancements in engineering CHO cell secretory machinery. The understanding of the mechanisms underlying the unique secretory function of antibody-producing plasma cells offers potential for further improvement in biopharmaceutical manufacturing.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Laura Bryan, Martin Clynes, Paula Meleady
Summary: CHO cells are commonly used host cell lines for producing human therapeutic proteins. Research has focused on improving growth, titre, and productivity of CHO cells to reduce production costs. Recent interest in CHO cell engineering has led to studies on post-translational modifications affecting protein functionality.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Biotechnology & Applied Microbiology
Stephen Bevan, Stefan Schoenfelder, Robert J. Young, Lin Zhang, Simon Andrews, Peter Fraser, Peter M. O'Callaghan
Summary: Chinese hamster ovary (CHO) cell lines are crucial for the biopharmaceutical industry, but their unstable transgene expression poses challenges. This study presents a 3D genome map of CHOK1SV (R) 10E9 cell line and an improved genome assembly, enhancing understanding of the CHO genome organization. Our findings reveal higher order chromatin structures and assist in identifying regulatory elements, ultimately improving transgene integration and cell line development.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Review
Biochemistry & Molecular Biology
Katja Glinsek, Kristof Bozovicar, Tomaz Bratkovic
Summary: CRISPR technology has made significant progress in CHO cell line engineering, improving protein production and product quality. It allows for glycosylation modulation, productivity enhancement, tackling adventitious agents, elimination of problematic host cell proteins, development of antibiotic-free selection systems, site-specific transgene integration, and CRISPR-mediated gene activation and repression. The review highlights the potential of CRISPR technology in CHO cell line genome editing and epigenetic engineering for more efficient and cost-effective development of biopharmaceuticals, ensuring the safety and quality of the final product.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Corey Kretzmer, Rajagopalan Lakshmi Narasimhan, Rahul Deva Lal, Vincent Balassi, James Ravellette, Ajaya Kumar Kotekar Manjunath, Jesvin Joy Koshy, Marta Viano, Serena Torre, Valeria M. Zanda, Mausam Kumravat, Keith Metelo Raul Saldanha, Harikrishnan Chandranpillai, Ifra Nihad, Fei Zhong, Yi Sun, Jason Gustin, Trissa Borgschulte, Jiajian Liu, David Razafsky
Summary: Chinese hamster ovary (CHO) cells have been the industry standard for therapeutic monoclonal antibody production. However, improving CHO cell lines has been difficult due to the cost and complexity of genome sequencing and gene editing tools. With the advancements in next-generation sequencing and the CRISPR/Cas9 system, it has become more feasible to sequence and manipulate the CHO genome, leading to the design of a more robust CHO cell line for cost-effective production of life-saving medications.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Plant Sciences
Biao Han, Longxin Wang, Yang Xian, Xiao-Man Xie, Wen-Qing Li, Ye Zhao, Ren-Gang Zhang, Xiaochun Qin, De-Zhu Li, Kai-Hua Jia
Summary: In this study, a high-quality genome of Quercus variabilis was generated using PacBio HiFi and Hi-C sequencing. The genome size was 787 Mb, with 12 pseudo-chromosomes. Q. variabilis was found to be closely related to Q. suber and no species-specific whole genome duplications were identified. These genomic resources will be valuable for breeding strategies and comparative genomics in oak species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Zhenyu Huang, Fei Shen, Yuling Chen, Ke Cao, Lirong Wang
Summary: The study presents a chromosome-scale genome assembly of Chinese plum, revealing the expansion of gene families associated with flavonoid metabolism and plant resistance. It suggests a domestication history of Chinese plum originating from South China and reconstructs the flavonoid-anthocyanin metabolism pathway through multi-omics analysis.
Article
Evolutionary Biology
Sandro Andreotti, Janine Altmueller, Claudia Quedenau, Tatiana Borodina, Geraldine Nouailles, Luiz Gustavo Teixeira Alves, Markus Landthaler, Maximilian Bieniara, Jakob Trimpert, Emanuel Wyler
Summary: The Roborovski dwarf hamster is a model for severe infection with the novel human coronavirus.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Johan B. Rojek, Yogesh Basavaraju, Saranya Nallapareddy, Dubhe B. B. Ocana, Roland Baumgartner, Sanne Schoffelen, Lise M. Grav, Steffen Goletz, Lasse E. Pedersen
Summary: This study demonstrates the application of Mad7 in CHO cells for gene knockout, expanding the versatility of the CRISPR toolbox for cell line engineering and research.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Pharmacology & Pharmacy
Shuang Cui, Huijian Hu, An Chen, Ming Cui, Xiaojie Pan, Pengfei Zhang, Guangji Wang, Hong Wang, Haiping Hao
Summary: The acetylation of FXR regulates its nucleocytoplasmic shuttling and degradation under conditions of liver injury, which limits the clinical benefits of FXR agonists. SIRT1 activators can reduce FXR acetylation and prevent its cytosolic degradation, and combining SIRT1 activators with FXR agonists shows promise in treating liver diseases.
ACTA PHARMACEUTICA SINICA B
(2023)
Article
Biotechnology & Applied Microbiology
Nathaniel. K. K. Hamaker, Kelvin. H. H. Lee
Summary: Efforts to improve CRISPR/Cas9 efficiency in targeted genomic modifications in mammalian cells led to the development of an all-in-one reporter system, including a new superfolder orange fluorescent protein (sfOrange), to quantify gene disruption, site-specific integration (SSI), and random integration (RI). Different donor plasmid formats and Cas9 nuclease variants were evaluated for accuracy and efficiency in Chinese hamster ovary cells. Double-cut and double-nick donor formats significantly improved targeting accuracy, and Cas9-mediated donor linearization increased RI events while donor nicking minimized RI without sacrificing SSI efficiency.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Review
Biotechnology & Applied Microbiology
Gene Schaefer, John Balchunas, Timothy Charlebois, John Erickson, Roger Hart, Sandeep B. Kedia, Kelvin H. Lee
Summary: The challenge of introducing new technologies into established industries is not unique to biopharmaceuticals, but it is crucial for the long-term competitiveness and delivery of therapies, particularly for new treatment modalities such as cell and gene therapies. This review identifies barriers to technology adoption and proposes enablers and suggestions for synergy and connection between innovation in product discovery and manufacturing, and across supplier, discovery, manufacturing, and regulatory arms.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
William Hilliard, Kelvin H. Lee
Summary: The use of targeted integration for industrial CHO cell line development requires significant upfront effort to identify genomic loci capable of supporting high therapeutic protein production. To address this barrier, the Transgene Integrated in Parallel screening method was used to characterize transgene expression from thousands of stable hotspots in the CHO genome. Cell lines with integrations at retargeted hotspot candidates consistently exhibited higher transgene mRNA expression than a commercially viable hotspot. These findings provide valuable resources for targeted integration platform development in the CHO community.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Chase E. Herman, Lie Min, Leila H. Choe, Ronald W. Maurer, Xuankuo Xu, Sanchayita Ghose, Kelvin H. H. Lee, Abraham M. Lenhoff
Summary: Recent research suggests that host-cell proteins (HCPs) and high molecular weight (HMW) species in monoclonal antibody downstream processing may be linked. Proteomic analysis reveals substantial overlap of HCP profiles between harvest cell culture fluid (HCCF) and protein A eluate, with HCPs conserved in aggregates that persist through the protein A capture step. These findings support previous hypotheses and highlight the importance of this persistence mechanism.
BIOTECHNOLOGY PROGRESS
(2023)
Article
Microbiology
Prasanna Joglekar, Barbra D. Ferrell, Tessa Jarvis, Kona Haramoto, Nicole Place, Jacob T. Dums, Shawn W. Polson, K. Eric Wommack, Jeffry J. Fuhrmann
Summary: The interactions between soybean bradyrhizobia and phages, as well as their impact on soybean yield, have been understudied compared to the well-studied bradyrhizobium-plant interactions.
Article
Biotechnology & Applied Microbiology
Young Hoon Oh, Kerri M. Mendola, Leila H. Choe, Lie Min, Ashton R. Lavoie, Sobhana A. Sripada, Taufika Islam Williams, Kelvin H. Lee, Yinges Yigzaw, Alexander Seay, Jerome Bill, Xuanwen Li, David J. Roush, Steven M. Cramer, Stefano Menegatti, Abraham M. Lenhoff
Summary: This study investigates the characterization and persistence of host-cell proteins (HCPs) in downstream processing steps for monoclonal antibody (mAb) manufacturing. The results show variability in HCP identities during processing steps, but consistency in the most abundant HCPs across different processes. The abundance of HCPs is likely related to the reproducibility of quantification measurements, and certain groups of HCPs may hinder characterization. The study suggests that factors such as HCP abundance and mAb-HCP interactions contribute to the persistence of individual HCPs and the identification of common, persistent HCPs in mAb manufacturing.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Qiang Fu, Yong Suk Lee, Erica A. Green, Yongdan Wang, So Young Park, Ashli Polanco, Kelvin H. Lee, Michael Betenbaugh, David McNally, Seongkyu Yoon
Summary: This study investigated the influence of four process parameters on the quality attributes of rAAV products. Regression models and a design space were established, and the predictive capability of the models was confirmed.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemical Research Methods
Chase E. Herman, Lie Min, Leila H. Choe, Ronald W. Maurer, Xuankuo Xu, Sanchayita Ghose, Kelvin H. Lee, Abraham M. Lenhoff
Summary: Recent research has revealed that aggregates in mAb solutions may contain not only mAb oligomers but also hundreds of host-cell proteins (HCPs), which suggests a relationship between aggregate persistence and HCP clearance during downstream purification operations. This study found that the phenomenon is relevant to depth filtration, protein A chromatography, and flow-through anion-exchange (AEX) polishing. Confocal laser scanning microscopy showed that aggregates compete with mAb during protein A chromatography, and column chromatography confirmed the presence of high aggregate concentrations in the protein A elution tail. Similar observations were made in flow-through AEX chromatography, with aggregate retention depending on resin surface chemistry. The quantification of aggregate mass fraction may serve as a surrogate for informing early process development decisions regarding HCP clearance strategies.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Review
Chemistry, Medicinal
Kang Wang, Yuecan Zhang, Guangji Wang, Haiping Hao, Hong Wang
Summary: Nonalcoholic fatty liver disease is a common liver disease without approved pharmacotherapy. Farnesoid X receptor (FXR) is considered a promising therapeutic target, but currently developed drugs have shown limited efficacy in clinical trials. This review summarizes the development of the FXR agonist obeticholic acid and discusses its limitations in depth.
MEDICINAL RESEARCH REVIEWS
(2023)
Article
Multidisciplinary Sciences
Dewi Pramanik, Annette Becker, Clemens Roessner, Oliver Rupp, Diego Bogarin, Oscar Alejandro Perez-Escobar, Anita Dirks-Mulder, Kevin Droppert, Alexander Kocyan, Erik Smets, Barbara Gravendeel
Summary: This study analyzes the evolution and development of fruit dehiscence zones in orchids. Gene expression analysis reveals that orchids have different fruit dehiscence mechanisms compared to Arabidopsis thaliana. Genes involved in carpel, gynoecium, ovule development, and lipid biosynthesis may play a novel role in the formation of dehiscence zone tissues in orchids.
Article
Plant Sciences
Lucie Schroeder, Oliver Rupp, Michael Senkler, Nils Rugen, Natalija Hohnjec, Alexander Goesmann, Helge Kuester, Hans-Peter Braun
Summary: European mistletoe is a hemiparasitic flowering plant with an extremely large genome size. A transcriptome project was conducted to study its gene space, resulting in a database containing sequences of thousands of open reading frames encoding distinct proteins. A new database, VaGs II, was developed by combining data from a summer and winter transcriptome project, and it showed a higher completeness compared to the previous database. The quality of the new database was evaluated by re-analyzing proteome data, which provided new insights into the oxidative phosphorylation system of European mistletoe.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
E. Anders Kiledal, Mark Shaw, Shawn W. Polson, Julia A. Maresca
Summary: This article introduces an improved DNA extraction method for concrete, which can efficiently extract DNA and reduce laboratory contamination. DNA extracted by this method was sequenced using the Illumina MiSeq system, revealing a microbial community dominated by halophilic bacteria and archaea in concrete, with enriched functional pathways related to osmotic stress responses. The study demonstrates that metagenomic sequencing can be used to characterize microbial communities in concrete, and older concrete structures may host different microbes compared to recently poured concrete.
MICROBIOLOGY SPECTRUM
(2023)
Article
Psychology, Multidisciplinary
Haiping Hao, Xiaobao Li, Xi Shen, Hong Jiang, Haoyue Xiao, Houchao Lyu
Summary: This study examined the reciprocal relationship between future time perspective and self-control among adolescents. The results showed that future-negative and future-confusional were negatively related to self-control, while future-positive, future-perspicuity, future-perseverant, and future-planning were positively related to self-control. The study also found reciprocal relationships between future-confusional, future-planning, and self-control.
CURRENT PSYCHOLOGY
(2023)
Article
Biochemical Research Methods
Lauren T. Cordova, Hussain Dahodwala, Rebecca Cooley, Kelvin H. Lee
Summary: In this study, researchers evaluated the expression of five DNA repair genes in over 40 CHO cell lines and found a correlation between two genes and cell line stability. Additionally, they found a negative correlation between the expression levels of DNA repair genes and cell age.
BIOTECHNOLOGY JOURNAL
(2023)
