Article
Biotechnology & Applied Microbiology
Fredrik Salmen, Joachim De Jonghe, Tomasz S. Kaminski, Anna Alemany, Guillermo E. Parada, Joe Verity-Legg, Ayaka Yanagida, Timo N. Kohler, Nicholas Battich, Floris van den Brekel, Anna L. Ellermann, Alfonso Martinez Arias, Jennifer Nichols, Martin Hemberg, Florian Hollfelder, Alexander van Oudenaarden
Summary: VASA-seq is a method that can detect the total transcriptome in single cells by fragmenting and tailing all RNA molecules after cell lysis. It is compatible with different experimental formats and can be used to analyze cell type markers, in vivo cell cycle, and alternative splicing, among others.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Hoang Van Phan, Michiel van Gent, Nir Drayman, Anindita Basu, Michaela U. Gack, Savas Tay
Summary: FD-seq is a high-throughput method for RNA sequencing of single cells fixed, stained, and sorted with paraformaldehyde, preserving RNA integrity and relative gene expression levels. This method can detect a higher number of genes and transcripts compared to methanol fixation, allowing for integration of phenotypic and transcriptomic information in rare cell subpopulations.
NATURE COMMUNICATIONS
(2021)
Review
Biochemical Research Methods
Michela Pulix, Vera Lukashchuk, Daniel C. Smith, Alan J. Dickson
Summary: HEK293 cell lines are being utilized for the production of recombinant proteins, virus-like particles and viral vectors, with ongoing advancements in molecular characterization and bioprocessing conditions to enhance their suitability for large-scale manufacture. These developments are positioning HEK293 cell systems as a critical platform for the production of future biologically based therapeutics, particularly in the field of gene therapy.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuanyuan Dou, Yan Lin, Tian-yun Wang, Xiao-Yin Wang, Yan-long Jia, Chun-peng Zhao
Summary: The combination of CMV enhancer with CAG promoter showed the highest efficiency for recombinant protein expression in HEK293F cells. Mild hypothermia post-transfection further increased the positive effect of CAG promoter on eGFP expression. CAG promoter outperformed CMV promoter in driving recombinant protein expression.
Article
Biochemical Research Methods
Elisa Godino, Ana Maria Restrepo Sierra, Christophe Danelon
Summary: The reconstitution of basic cellular functions in micrometer-sized liposomes has sparked interest in constructing synthetic cells. Microscopy and flow cytometry have limitations when used separately to study biological processes in liposomes, requiring a compromise between information-rich imaging and statistical analysis. To overcome this, imaging flow cytometry (IFC) is introduced for high-throughput, microscopy-based screening of gene-expressing liposomes in laminar flow. A comprehensive pipeline and analysis toolset based on a commercial IFC instrument and software were developed, allowing for robust population statistics and quantification of complex phenotypes relevant for synthetic cell construction. The general applicability, current workflow limitations, and future prospects of IFC in synthetic cell research are discussed.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Dongwoo Kim, Seul Mi Kim, Jaejin Lee, Jiwon Kim, Jae Seong Lee
Summary: Plasmid-based transfection can be used to improve transient gene expression (TGE) in mammalian cells. By knocking out the lysosomal membrane protein LAMP2C, intracellular plasmid availability was significantly increased, leading to enhanced TGE-based recombinant protein expression in HEK293 cells.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Zhuo-Xing Shi, Zhi-Chao Chen, Jia-Yong Zhong, Kun-Hua Hu, Ying-Feng Zheng, Ying Chen, Shang-Qian Xie, Xiao-Chen Bo, Feng Luo, Chong Tang, Chuan-Le Xiao, Yi-Zhi Liu
Summary: Long-read single-cell RNA isoform sequencing can reveal the complex landscape of alternative RNA splicing in individual cells, but it has a low read throughput. The authors developed circular consensus sequencing methods to achieve high-throughput and high-accuracy single-cell RNA isoform sequencing.
NATURE COMMUNICATIONS
(2023)
Article
Virology
Eduard Puente-Massaguer, Byron Cajamarca-Berrezueta, Aleix Volart, Irene Gonzalez-Dominguez, Francesc Godia
Summary: This study explores the production of Gag VLPs with the BacMam expression system in a suspension culture of HEK293 cells and determines the optimal culture conditions. The results show that high cell transduction efficiency and VLP production can be achieved under optimal conditions, and the characteristics of the produced VLPs are validated using super-resolution fluorescence microscopy. Evidence of different pathways for BacMam transduction is also provided. This work lays the foundation for future research aiming to scale up the BacMam baculovirus system as an alternative strategy for VLP production.
Article
Chemistry, Analytical
Sang-Yun Lee, Hyun Ju Hwang, Bosung Ku, Dong Woo Lee
Summary: The use of the CPRE 3D-HTS model improves the correlation of EGFR-targeting drugs compared to 2D cell-based HTS. In breast cancer cell lines, the CPRE 3D-HTS model shows a greater difference in the expression of HER2 protein between HER2-positive and HER2-negative cells. Alginate was selected as the extracellular matrix to enhance cell proliferation receptor expression in the CPRE 3D-HTS model.
ANALYTICAL CHEMISTRY
(2022)
Article
Biophysics
V. P. Sangeetha, Sri Smriti, Pratima R. Solanki, P. Mohanan
Summary: The study revealed that at higher concentrations, zwitterionic carbon dots can affect cell viability and mitochondrial membrane potential, leading to apoptosis, with higher concentrations resulting in a higher percentage of apoptosis.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Article
Biochemistry & Molecular Biology
Beata Flachner, Krisztina Dobi, Anett Benedek, Sandor Cseh, Zsolt Lorincz, Istvan Hajdu
Summary: This paper describes the expression of RI in baculovirus-infected High Five cells and compares the differences between RI expressed in insect cells and commercially available products. The results show that RI expressed in insect cells has higher thermal stability and is endotoxin-free, making it potentially useful for future therapeutics.
Article
Multidisciplinary Sciences
Meng Zhang, Mary Elisabeth Ehmann, Srija Matukumalli, Aashutosh Girish Boob, David M. Gilbert, Huimin Zhao
Summary: Chromatin boundary elements are difficult to define and characterize. Here the authors report Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains (SHIELD) for high-throughput screening of barrier-type DNA elements in human cells.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Chelsea Mayoh, Jie Mao, Jinhan Xie, Gabor Tax, Shu-Oi Chow, Roxanne Cadiz, Karina Pazaky, Paulette Barahona, Pamela Ajuyah, Peter Trebilcock, Angela Malquori, Kate Gunther, Anica Avila, Doo Young Yun, Stephanie Alfred, Anjana Gopalakrishnan, Alvin Kamili, Marie Wong, Mark J. Cowley, Sophie Jessop, Loretta M. S. Lau, Toby N. Trahair, David S. Ziegler, Jamie I. Fletcher, Andrew J. Gifford, Maria Tsoli, Glenn M. Marshall, Michelle Haber, Vanessa Tyrrell, Timothy W. Failes, Greg M. Arndt, Richard B. Lock, Paul G. Ekert, M. Emmy M. Dolman
Summary: One-third of pediatric cancer patients enrolled in precision medicine programs do not receive therapeutic recommendations from molecular profiling. In order to find potential strategies for treating high-risk pediatric patients, a study conducted in vitro screening of 125 patient-derived samples against a library of 126 anticancer drugs. The results showed that high-throughput drug screening (HTS) can identify effective biomarker-driven therapeutic strategies for high-risk pediatric cancers.
Article
Chemistry, Analytical
Shiyu Wang, Yang Liu, Yijian Li, Menghua Lv, Kai Gao, Ying He, Wenbo Wei, Yonggang Zhu, Xuan Dong, Xun Xu, Zida Li, Longqi Liu, Ya Liu
Summary: The study presents a droplet-based microfluidic platform for efficient screening and sorting of tumor antigen-specific T cells, demonstrating high throughput capability and validation through single-cell RNA sequencing. The platform offers a precise and efficient means for T cell immunotherapy, potentially promoting T cell-based anti-tumor therapies.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Jongmin Woo, Sarah M. Williams, Lye Meng Markillie, Song Feng, Chai-Feng Tsai, Victor Aguilera-Vazquez, Ryan L. Sontag, Ronald J. Moore, Dehong Hu, Hardeep S. Mehta, Joshua Cantlon-Bruce, Tao Liu, Joshua N. Adkins, Richard D. Smith, Geremy C. Clair, Ljiljana Pasa-Tolic, Ying Zhu
Summary: This study introduces a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based single-cell proteomics workflow. The N2 chip enables robust quantification of approximately 1500 proteins and reveals membrane protein markers, demonstrating high stability of single-cell proteome profiles for cells cultured under identical conditions.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Jiandong Huo, Yuguang Zhao, Jingshan Ren, Daming Zhou, Helen M. E. Duyvesteyn, Helen M. Ginn, Loic Carrique, Tomas Malinauskas, Reinis R. Ruza, Pranav N. M. Shah, Tiong Kit Tan, Pramila Rijal, Naomi Coombes, Kevin R. Bewley, Julia A. Tree, Julika Radecke, Neil G. Paterson, Piyada Supasa, Juthathip Mongkolsapaya, Gavin R. Screaton, Miles Carroll, Alain Townsend, Elizabeth E. Fry, Raymond J. Owens, David Stuart
CELL HOST & MICROBE
(2020)
Article
Biochemistry & Molecular Biology
Daming Zhou, Helen M. E. Duyvesteyn, Cheng-Pin Chen, Chung-Guei Huang, Ting-Hua Chen, Shin-Ru Shih, Yi-Chun Lin, Chien-Yu Cheng, Shu-Hsing Cheng, Yhu-Chering Huang, Tzou-Yien Lin, Che Ma, Jiandong Huo, Loic Carrique, Tomas Malinauskas, Reinis R. Ruza, Pranav N. M. Shah, Tiong Kit Tan, Pramila Rijal, Robert F. Donat, Kerry Godwin, Karen R. Buttigieg, Julia A. Tree, Julika Radecke, Neil G. Paterson, Piyada Supasa, Juthathip Mongkolsapaya, Gavin R. Screaton, Miles W. Carroll, Javier Gilbert-Jaramillo, Michael L. Knight, William James, Raymond J. Owens, James H. Naismith, Alain R. Townsend, Elizabeth E. Fry, Yuguang Zhao, Jingshan Ren, David Stuart, Kuan-Ying A. Huang
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Jiangdong Huo, Audrey Le Bas, Reinis R. Ruza, Helen M. E. Duyvesteyn, Halina Mikolajek, Tomas Malinauskas, Tiong Kit Tan, Pramila Rijal, Maud Dumoux, Philip N. Ward, Jingshan Ren, Daming Zhou, Peter J. Harrison, Miriam Weckener, Daniel K. Clare, Vinod K. Vogirala, Julika Radecke, Lucile Moynie, Yuguang Zhao, Javier Gilbert-Jaramillo, Michael L. Knight, Julia A. Tree, Karen R. Buttigieg, Naomi Coombes, Michael J. Elmore, Miles W. Carroll, Loic Carrique, Pranav N. M. Shah, William James, Alain R. Townsend, David Stuart, Raymond J. Owens, James H. Naismith
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Article
Immunology
Simon P. Graham, Rebecca K. McLean, Alexandra J. Spencer, Sandra Belij-Rammerstorfer, Daniel Wright, Marta Ulaszewska, Jane C. Edwards, Jack W. P. Hayes, Veronica Martini, Nazia Thakur, Carina Conceicao, Isabelle Dietrich, Holly Shelton, Ryan Waters, Anna Ludi, Ginette Wilsden, Clare Browning, Dagmara Bialy, Sushant Bhat, Phoebe Stevenson-Leggett, Philippa Hollinghurst, Ciaran Gilbride, David Pulido, Katy Moffat, Hannah Sharpe, Elizabeth Allen, Valerie Mioulet, Chris Chiu, Joseph Newman, Amin S. Asfor, Alison Burman, Sylvia Crossley, Jiandong Huo, Raymond J. Owens, Miles Carroll, John A. Hammond, Elma Tchilian, Dalan Bailey, Bryan Charleston, Sarah C. Gilbert, Tobias J. Tuthill, Teresa Lambe
Article
Biochemistry & Molecular Biology
Corey R. Nelson, Tyler Mrozowich, Sean M. Park, Simmone D'souza, Amy Henrickson, Justin R. J. Vigar, Hans-Joachim Wieden, Raymond J. Owens, Borries Demeler, Trushar R. Patel
Summary: This study demonstrates that DDX17 can directly interact with and unwind RVFV non-coding RNA regions IGR and NCR, providing important insights into the mechanism by which DDX17 restricts RVFV replication.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Tiong Kit Tan, Pramila Rijal, Rolle Rahikainen, Anthony H. Keeble, Lisa Schimanski, Saira Hussain, Ruth Harvey, Jack W. P. Hayes, Jane C. Edwards, Rebecca K. McLean, Veronica Martini, Miriam Pedrera, Nazia Thakur, Carina Conceicao, Isabelle Dietrich, Holly Shelton, Anna Ludi, Ginette Wilsden, Clare Browning, Adrian K. Zagrajek, Dagmara Bialy, Sushant Bhat, Phoebe Stevenson-Leggett, Philippa Hollinghurst, Matthew Tully, Katy Moffat, Chris Chiu, Ryan Waters, Ashley Gray, Mehreen Azhar, Valerie Mioulet, Joseph Newman, Amin S. Asfor, Alison Burman, Sylvia Crossley, John A. Hammond, Elma Tchilian, Bryan Charleston, Dalan Bailey, Tobias J. Tuthill, Simon P. Graham, Helen M. E. Duyvesteyn, Tomas Malinauskas, Jiandong Huo, Julia A. Tree, Karen R. Buttigieg, Raymond J. Owens, Miles W. Carroll, Rodney S. Daniels, John W. McCauley, David I. Stuart, Kuan-Ying A. Huang, Mark Howarth, Alain R. Townsend
Summary: This study introduces a potential vaccine candidate against SARS-CoV-2, utilizing a synthetic virus-like particle platform to present the receptor-binding domain of the virus spike protein. The vaccine induces strong neutralizing antibody responses in mice and pigs, demonstrating thermostability and the potential for global distribution.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Joanne L. Parker, Justin C. Deme, Gabriel Kuteyi, Zhiyi Wu, Jiandong Huo, I. David Goldman, Raymond J. Owens, Philip C. Biggin, Susan M. Lea, Simon Newstead
Summary: Folates, also known as vitamin B9, play a critical role in cellular metabolism and their deficiency is linked to various disorders. Mammals cannot synthesize folates and rely on uptake from the diet. The proton-coupled folate transporter is important for folate uptake and drug delivery.
Article
Multidisciplinary Sciences
Joanne L. Parker, Justin C. Deme, Zhiyi Wu, Gabriel Kuteyi, Jiandong Huo, Raymond J. Owens, Philip C. Biggin, Susan M. Lea, Simon Newstead
Summary: The proton-coupled solute carriers PepT1 and PepT2 in the SLC15 family are crucial for acquiring dietary nitrogen and have extreme substrate promiscuity. Recent studies on their structure and function provide insights into their potential applications in drug development.
Article
Multidisciplinary Sciences
Petra Lukacik, C. David Owen, Gemma Harris, Jani Reddy Bolla, Sarah Picaud, Irfan Alibay, Joanne E. Nettleship, Louise E. Bird, Raymond J. Owens, Philip C. Biggin, Panagis Filippakopoulos, Carol Robinson, Martin A. Walsh
Summary: The crystal structure of SapA, a component of the important Sap ABC transporter system in NTHi, has been found to be in a closed, ligand bound conformation, with its central ligand binding cavity likely occupied by di- or tri-peptides. Surface interactions between SapA and heme and dsRNA were observed, suggesting a potential role for SapA in the transport of di- or tri-peptides.
Review
Virology
Qilong Tang, Raymond J. Owens, James H. Naismith
Summary: Nanobodies, derived from heavy-chain-only subclass of Camelid immunogloblins, are small-sized molecules with high affinity and stability, making them unique targeting reagents in biomedical sciences. With the rapid spread of SARS-CoV-2, nanobodies directed against the viral Spike protein have shown promising results in neutralizing the virus, with some agents already undergoing clinical trials. Researchers are studying the structural features guiding nanobody recognition to develop effective treatments against the pandemic.
Article
Chemistry, Medicinal
Indran Mathavan, Lawrence J. Liu, Sean W. Robinson, Nelly El-Sakkary, Adam Jo J. Elatico, Darwin Gomez, Ricky Nellas, Raymond J. Owens, William Zuercher, Iva Navratilova, Conor R. Caffrey, Konstantinos Beis
Summary: Schistosomiasis is a neglected tropical disease caused by parasitic flatworms. Treatment options are limited, but the study identifies SmVKR2 as a potential drug target. Screening of inhibitors against SmVKR2 led to the identification of compounds that could inhibit its enzymatic activity and induce phenotypic changes in the parasite.
ACS MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Ecology
Bhumika S. S. Shah, Benjamin A. A. Ford, Deepa Varkey, Halina Mikolajek, Christian Orr, Vitaliy Mykhaylyk, Raymond J. J. Owens, Ian T. T. Paulsen
Summary: Despite low surface concentrations, phosphorus (P) availability in marine environments is crucial for biological processes. Picocyanobacteria strains possess a putative phosphorus transporter, PhnDCE, but lack the ability to degrade phosphite or utilize alternate phosphorus sources. Our study found that Synechococcus PhnD1 proteins selectively bind phosphorus compounds, with a higher affinity for phosphite. However, growth experiments showed that Synechococcus strains cannot utilize phosphite as a sole phosphorus source, suggesting that the PhnDCE transporter is a constitutively expressed, medium-affinity phosphate transporter.
Article
Biochemistry & Molecular Biology
Jagan Mohan Kaipa, Ganna Krasnoselska, Raymond J. J. Owens, Joop van den Heuvel
Summary: This study compares the small-scale production of six selected eukaryotic integral membrane proteins in insect and mammalian cell expression systems using different techniques for gene delivery. The choice of expression systems has a significant impact on the yield and quality of the target proteins. Virus-free transient gene expression in insect High Five cells combined with solubilization in dodecylmaltoside plus cholesteryl hemisuccinate generated the most homogeneous samples for all six targets. TGE in High Five insect cells offers a fast and economically attractive alternative for the production of integral membrane proteins.
Review
Biochemistry & Molecular Biology
Milos Hricovini, Raymond J. Owens, Andrzej Bak, Violetta Kozik, Witold Musial, Roberta Pierattelli, Magdalena Majekova, Yoel Rodriguez, Robert Musiol, Aneta Slodek, Pavel Starha, Karina Pietak, Dagmara Slota, Wioletta Florkiewicz, Agnieszka Sobczak-Kupiec, Josef Jampilek
Summary: Knowledge of interactions between molecules is crucial for the advancement of biomedical and biological sciences. Chemical biology/biological chemistry serves as an interdisciplinary bridge, connecting the perspectives of chemistry and biology in the study of small molecules/peptidomimetics and their interactions in biological systems. Understanding the atomic structure and molecular properties in the context of cellular environment is vital for the design of highly druggable and drug-like medicines.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Angeliki Ditsiou, Chiara Cilibrasi, Nikiana Simigdala, Athanasios Papakyriakou, Leanne Milton-Harris, Viviana Vella, Joanne E. Nettleship, Jae Ho Lo, Shivani Soni, Goar Smbatyan, Panagiota Ntavelou, Teresa Gagliano, Maria Chiara Iachini, Sahir Khurshid, Thomas Simon, Lihong Zhou, Storm Hassell-Hart, Philip Carter, Laurence H. Pearl, Robin L. Owen, Raymond J. Owens, S. Mark Roe, Naomi E. Chayen, Heinz-Josef Lenz, John Spencer, Chrisostomos Prodromou, Apostolos Klinakis, Justin Stebbing, Georgios Giamas