Article
Multidisciplinary Sciences
Oskar Staufer, Franziska Dietrich, Rahul Rimal, Martin Schroeter, Sebastian Fabritz, Heike Boehm, Smriti Singh, Martin Moeller, Ilia Platzman, Joachim Pius Spatz
Summary: Extracellular vesicles play a crucial role in intercellular communication and cell physiology, but quantitative knowledge on their signaling mechanisms is lacking, hampering their therapeutic applications. By using a synthetic approach, researchers have shown that synthetic EVs have functionalities similar to natural EVs and can be used for therapeutic purposes in wound healing and neovascularization. Transcriptome profiling has enabled a systematic decoding of synergistic effects between individual EV constituents, leading to a better understanding of EV signaling.
Article
Engineering, Biomedical
Jochen Estebano Hernandez Buecher, Oskar Staufer, Lukas Ostertag, Ulrike Mersdorf, Ilia Platzman, Joachim Pius Spatz
Summary: This article describes a bottom-up approach for the controlled assembly of fully-synthetic immune-inspired cells using predefined molecular components, reducing the complexity of the immune system. The study demonstrates the effectiveness of these synthetic immune cells through structural and functional characterization, providing new learning-by-building approaches in synthetic immunology.
Article
Chemistry, Multidisciplinary
Kevin Jahnke, Vanessa Huth, Ulrike Mersdorf, Na Liu, Kerstin Goepfrich
Summary: In this study, artificial DNA-based cytoskeletons with programmed multifunctionality were assembled inside synthetic cells using light-controlled assembly and disassembly. By using molecular crowders, ordered bundling of DNA filaments and formation of ring-like cortical structures similar to actin rings during cell division were achieved. Additionally, DNA filaments were programmably linked to the compartment periphery using cholesterol-tagged DNA and were able to deform GUVs from within.
Article
Biotechnology & Applied Microbiology
Xiumin Ding, Zhiming Zheng, Genhai Zhao, Li Wang, Han Wang, Qiang Yang, Mengxue Zhang, Luyao Li, Peng Wang
Summary: In this study, a synthetic strain with high efficiency, low carbon, and cofactor recycling for MK-7 synthesis was constructed using synthetic biology methods. The synthetic redesign of the synthesis pathway and optimization of material and energy metabolism improved the production of MK-7. The strategy used in this study can be applied to the construction of high-efficiency synthesis platforms for other terpenoids, paving the way for large-scale production of MK-7 and other valuable terpenoids.
MICROBIAL CELL FACTORIES
(2022)
Article
Biology
Oskar Staufer, Jacqueline A. de Lora, Eleonora Bailoni, Alisina Bazrafshan, Amelie S. Benk, Kevin Jahnke, Zachary A. Manzer, Lado Otrin, Telmo Diez Perez, Judee Sharon, Jan Steinkuhler, Katarzyna P. Adamala, Bruna Jacobson, Marileen Dogterom, Kerstin Gopfrich, Darko Stefanovic, Susan R. Atlas, Michael Grunze, Matthew R. Lakin, Andrew P. Shreve, Joachim P. Spatz, Gabriel P. Lopez
Summary: The 'learning-by-building' approach, which combines concepts from physics, chemistry and bioengineering, is gaining popularity in the life sciences field, particularly among researchers trying to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from various disciplines to showcase advancements and challenges in the field of synthetic cells, emphasizing the importance of building an international and interdisciplinary research community.
Review
Pharmacology & Pharmacy
Malvin L. Pardi, Juanqi Wu, Shunsuke Kawasaki, Hirohide Saito
Summary: This review discusses recent developments of RNA-based synthetic genetic circuits in mammalian cells, including post-transcriptional control methods and auxiliary components, as well as their applications in biomedical and preclinical settings.
ADVANCED DRUG DELIVERY REVIEWS
(2022)
Review
Biotechnology & Applied Microbiology
Mariana Hernandez-Elvira, Per Sunnerhagen
Summary: To remain competitive, cells need to balance growth and proliferation with stress protection. Different levels of gene expression control are engaged in stress responses depending on the time scale of stress exposure. Post-transcriptional control is appropriate for minute-scale responses to transient stress and recovery. It regulates the turnover rate, translational activity, covalent modifications, and subcellular localization of RNA species through multiple cellular pathways to achieve appropriate signaling intensity, avoid undue triggering of stress-activated pathways, and timely down-regulate the response.
FEMS YEAST RESEARCH
(2022)
Review
Biochemical Research Methods
Mattia Furlan, Stefano de Pretis, Mattia Pelizzola
Summary: Despite RNA abundance being commonly assumed as a proxy for transcriptional activity, it is now possible to calculate how synthesis, processing, and degradation rates collectively determine the abundance of each gene's RNA. Different transcriptional outputs can correspond to different combinations of kinetic rates, indicating the existence of markedly different modes of gene expression regulation and their profound effects on gene self-expression regulation.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Jaeyoung K. Jung, Blake J. Rasor, Grant A. Rybnicky, Adam D. Silverman, Janet Standeven, Robert Kuhn, Teresa Granito, Holly M. Ekas, Brenda M. Wang, Ashty S. Karim, Julius B. Lucks, Michael C. Jewett
Summary: As the field of synthetic biology expands, the need to grow and train STEM practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. To address this, shelf-stable cell-free biosensing educational modules were developed, allowing students to create their own bioengineered systems by adding water and DNA to freeze-dried crude extracts of non-pathogenic Escherichia coli. This work promises to increase access to interactive synthetic biology education opportunities.
ACS SYNTHETIC BIOLOGY
(2023)
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Article
Chemistry, Multidisciplinary
Ana Yagu''e Relimpio, Andreas Fink, Duc Thien Bui, Sebastian Fabritz, Martin Schro''ter, Alessia Ruggieri, Ilia Platzman, Joachim P. Spatz
Summary: This study uses bottom-up assembled synthetic SARS-CoV-2 viruses to investigate the binding properties of the Omicron and Alpha variants. The results reveal a significantly higher affinity of Omicron S towards the lipid membrane and ACE2 receptor.
Article
Biochemistry & Molecular Biology
Pasquale Stano, Pier Luigi Gentili, Luisa Damiano, Maurizio Magarini
Summary: This paper discusses the potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) and highlights the central role of Synthetic Biology (SB). Bottom-up SCs have the ability to be designed and tailored, allowing for chemical exchange with other cells or biological cells.
Article
Chemistry, Multidisciplinary
Roger Rubio-Sanchez, Giacomo Fabrini, Pietro Cicuta, Lorenzo Di Michele
Summary: DNA nanotechnology is used to construct biomimetic nanomachines that are essential for creating complex cell-like entities from the bottom-up. Recent efforts focus on designing biomimetic membrane-anchored DNA nanostructures to impart complex functionalities to cell-like objects.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biology
Vivek Kumar Raxwal, Somya Singh, Manu Agarwal, Karel Riha
Summary: The study revealed that new genes in rice have relatively low expression levels, possibly controlled by distal enhancers and chromatin conformation at their TSS; the chromatin in TSS regions may be remodeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis are prone to nonsense-mediated RNA decay, restricting their expression.
Article
Biochemical Research Methods
Andres F. Lopez-Lopera, Nicolas Durrande, Mauricio A. Alvarez
Summary: The regulatory process of Drosophila is studied using physically-inspired stochastic models, focusing on post-transcriptional events. Two different Gaussian processes models are investigated based on reaction-diffusion equations, with performance assessments on high-resolution datasets.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Cell Biology
Susanna Croci, Mary Anna Venneri, Stefania Mantovani, Chiara Fallerini, Elisa Benetti, Nicola Picchiotti, Federica Campolo, Francesco Imperatore, Maria Palmieri, Sergio Daga, Chiara Gabbi, Francesca Montagnani, Giada Beligni, Ticiana D. J. Farias, Miriam Lucia Carriero, Laura Di Sarno, Diana Alaverdian, Sigrid Aslaksen, Maria Vittoria Cubellis, Ottavia Spiga, Margherita Baldassarri, Francesca Fava, Paul J. Norman, Elisa Frullanti, Andrea M. Isidori, Antonio Amoroso, Francesca Mari, Simone Furini, Mario U. Mondelli, Mario Chiariello, Alessandra Renieri, Ilaria Meloni
Summary: The L412F polymorphism in TLR3 is associated with severity of COVID-19, particularly in males. Research has shown that this polymorphism affects immune system autophagy activity and reduces production of certain cytokines, while also increasing the risk of developing autoimmune diseases in COVID-19 patients.
Article
Genetics & Heredity
Stefania Mantovani, Sergio Daga, Chiara Fallerini, Margherita Baldassarri, Elisa Benetti, Nicola Picchiotti, Francesca Fava, Anna Galli, Silvia Zibellini, Mirella Bruttini, Maria Palmieri, Susanna Croci, Sara Amitrano, Diana Alaverdian, Katia Capitani, Simone Furini, Francesca Mari, Ilaria Meloni, Elisa Frullanti, Mario U. Mondelli, Alessandra Renieri
Summary: TLR7 variants in male patients lead to impaired immune response to viruses like SARS-CoV-2, resulting in severe COVID-19. These variants cause significant damage to the TLR7 signaling pathway and hinder the type I and II interferon responses.
GENES AND IMMUNITY
(2022)
Article
Genetics & Heredity
Chiara Fallerini, Nicola Picchiotti, Margherita Baldassarri, Kristina Zguro, Sergio Daga, Francesca Fava, Elisa Benetti, Sara Amitrano, Mirella Bruttini, Maria Palmieril, Susanna Croci, Mirjam Lista, Giada Beligni, Floriana Valentino, Ilaria Meloni, Marco Tanfoni, Francesca Minnai, Francesca Colombo, Enrico Cabri, Maddalena Fratelli, Chiara Gabbi, Stefania Mantovani, Elisa Frullanti, Marco Gori, Francis P. Crawley, Guillaume Butler-Laporte, Brent Richards, Hugo Zeberg, Miklos Lipcsey, Michael Hultstrom, Kerstin U. Ludwig, Eva C. Schulte, Erola Pairo-Castineira, John Kenneth Baillie, Axel Schmidt, Robert Frithiof, Francesca Mari, Alessandra Renieri, Simone Furini
Summary: The study developed a machine-learning model using common and rare exonic variants to predict COVID-19 severity. By selecting key Boolean features and combining them into an Integrated PolyGenic Score, the model offers insights into the genetic contribution to disease severity. A quarter of the selected genes are sex-specific, and pathway analysis highlighted the multi-organ nature of COVID-19 severity. This model could potentially aid in diagnostics, therapeutics, and disease management at the bedside.
Article
Biotechnology & Applied Microbiology
Pasqualina Scala, J. Lovecchio, E. P. Lamparelli, R. Vitolo, V Giudice, E. Giordano, C. Selleri, L. Rehak, N. Maffulli, G. Della Porta
Summary: An in-vitro model of human bone marrow mesenchymal stem cells (hBM-MSCs) myogenic commitment was developed using static co-seeding and perfused culture systems. Static co-seeding showed a significant increase in gene expression, while the myogenic induction ability of hSkMs on hBM-MSCs under perfusion conditions was mainly exerted through paracrine effect. The dynamic culture also resulted in a significant increase in anti-inflammatory cytokine gene expression, confirming the immunomodulatory activity of hBM-MSCs along with commitment events.
ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
J. Lovecchio, V Betti, M. Cortesi, E. Ravagli, S. Severi, E. Giordano
Summary: Monitoring the maturation of bone tissue engineered constructs is crucial for ensuring their quality. Traditional destructive methods require sacrificing samples, while light spectroscopy-based methods provide non-destructive monitoring. In this study, a miniaturized and inexpensive custom-made spectrometer device is proposed for real-time/in-line analysis and integration with bioreactor systems.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Kristina Zguro, Chiara Fallerini, Francesca Fava, Simone Furini, Alessandra Renieri
Summary: The COVID-19 pandemic has had a significant impact on global public health, societies, and economies. Understanding the disease better is crucial, and international collaborations have identified genetic markers that explain the varied clinical outcomes and can guide the development of diagnostics and therapeutics.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Chemistry, Physical
Joseph Lovecchio, Marilisa Cortesi, Marco Zani, Marco Govoni, Dante Dallari, Emanuele Giordano
Summary: 3D printing has provided new opportunities for the fabrication of biocompatible hybrid pseudo-tissues. This study focuses on modifying a commercial 3D printer into a 3D bioplotter to control scaffold fiber thickness and porosity. The results demonstrate the feasibility of printing hydrogels commonly used for cell culture and tissue engineering applications.
Letter
Genetics & Heredity
Lucia Pia Bruno, Gabriella Doddato, Margherita Baldassarri, Caterina Lo Rizzo, Sara Resciniti, Mirella Bruttini, Lista Mirjam, Kristina Zguro, Simone Furini, Maria Antonietta Mencarelli, Alessandra Renieri, Francesca Ariani
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Correction
Biochemistry & Molecular Biology
Sergio Daga, Francesco Donati, Katia Capitani, Susanna Croci, Rossella Tita, Annarita Giliberti, Floriana Valentino, Elisa Benetti, Chiara Fallerini, Francesca Niccheri, Margherita Baldassarri, Maria Antonietta Mencarelli, Elisa Frullanti, Simone Furini, Silvestro Giovanni Conticello, Alessandra Renieri, Anna Maria Pinto
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Correction
Biochemistry & Molecular Biology
Susanna Croci, Miriam Lucia Carriero, Katia Capitani, Sergio Daga, Francesco Donati, Elisa Frullanti, Vittoria Lamacchia, Rossella Tita, Annarita Giliberti, Floriana Valentino, Elisa Benetti, Annalisa Ciabattini, Simone Furini, Caterina Lo Rizzo, Anna Maria Pinto, Silvestro Giovanni Conticello, Alessandra Renieri, Ilaria Meloni
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Chemistry, Medicinal
Francesco Pettini, Carmen Domene, Simone Furini
Summary: Fast C-type inactivation confers distinctive functional properties to the hERG potassium channel, but its mechanism and association with cardiac arrythmias are of paramount importance. Two models have been proposed for C-type inactivation in K+ channels, and this study used molecular dynamics simulations to investigate the mechanism in hERG. The findings suggest that C-type inactivation in hERG involves a widening of the extracellular entrance of the channel rather than a closure of the selectivity filter.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Correction
Oncology
Chiara Fallerini, Sergio Daga, Elisa Benetti, Nicola Picchiotti, Kristina Zguro, Francesca Catapano, Virginia Baroni, Simone Lanini, Alessandro Bucalossi, Giuseppe Marotta, Francesca Colombo, Margherita Baldassarri, Francesca Fava, Giada Beligni, Laura Di Sarno, Diana Alaverdian, Maria Palmieri, Susanna Croci, Andrea M. M. Isidori, Simone Furini, Elisa Frullanti, Alessandra GEN-COVID Multictr Study, Alessandra Renieri, Francesca Mari
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Roberto Di Blasi, Mara Pisani, Fabiana Tedeschi, Masue M. Marbiah, Karen Polizzi, Simone Furini, Velia Siciliano, Francesca Ceroni
Summary: Resource competition can cause unintended coupling between co-expressed genetic constructs. In this study, the authors quantified the resource load of different mammalian genetic components, identifying construct designs with increased performance and reduced resource footprint. By generating improved synthetic circuits and optimizing the co-expression of transfected cassettes, this work sheds light on their usefulness in bioproduction and biotherapeutic applications.
NATURE COMMUNICATIONS
(2023)
Article
Psychiatry
Flavia Privitera, Maria A. Trusso, Floriana Valentino, Gabriella Doddato, Chiara Fallerini, Giulia Brunelli, Romina D'Aurizio, Simone Furini, Arianna Goracci, Andrea Fagiolini, Francesca Mari, Alessandra Renieri, Francesca Ariani
Summary: This study focuses on a large family with 12 members affected by bipolar disorder. Through whole-exome sequencing, certain genes, including CLN6 and ZNF92, were identified as having variations associated with the disorder. The findings suggest that heterozygous carriers of CLN6 may develop bipolar disorder later in life if combined with additional variants in ZNF92.
BRAZILIAN JOURNAL OF PSYCHIATRY
(2023)
Article
Chemistry, Medicinal
Francesco Pettini, Carmen Domene, Simone Furini
Summary: The study of the inactivation mechanism of hERG is crucial due to its association with cardiac arrhythmias. Two models, namely, the closure of the selectivity filter and the widening of the extracellular portion of the selectivity filter, have been proposed to describe C-type inactivation in potassium channels. Molecular dynamics simulations revealed that the extracellular entrance of hERG widens during inactivation, supporting the hypothesis of widening of the extracellular entrance rather than closure of the selectivity filter.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
