Article
Biology
Alejandra Rojas Lopez, Pablo Monzon, Luis Acerenza
Summary: Apoptosis, a highly regulated cell death process, remains incompletely understood, particularly in terms of the intrinsic pathway. Using a differential equations model, this study found that the transcription factor E2F plays a critical role in regulating apoptosis activation by directly influencing the synthesis rates of key proteins such as caspase 3 and caspase 9. Sensitivity analysis showed that the concentration of E2F determines whether apoptosis is possible, with low E2F levels preventing apoptosis and high E2F levels leading to inevitable apoptosis activation.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Engineering, Environmental
Diwu Fan, Yong Sun, Moxian Chen, Yongli Zhu, Evgenios Agathokleous, Fuyuan Zhu, Jiangang Han
Summary: This study aimed to identify and verify key genes in regulating Cd-induced hormesis in Arabidopsis thaliana. The results showed that hormesis occurred at certain concentrations of Cd, and the antioxidant defense system and photosynthesis system played roles in hormesis. The key gene ABF1 in the metabolic pathway of abscisic acid was identified and found to be essential for Cd-induced hormesis.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Cell Biology
Alexandra D. Buffry, Sebastian Kittelmann, Alistair P. McGregor
Summary: Hox genes determine the regional identity of animal bodies during embryogenesis and play a role in post-embryonic fine-scale morphology. In Drosophila melanogaster, the Ultrabithorax (Ubx) gene regulates bristle and trichome patterning on the femurs of the second and third leg pairs. The repression of trichomes in the proximal posterior region of the T2 femur by Ubx is mediated by the activation of microRNA-92a and microRNA-92b. Additionally, a novel enhancer of Ubx that recapitulates its temporal and regional activity in T2 and T3 legs has been identified, along with transcription factors and co-factors that regulate trichome patterning.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Hongzhang Wang, Zhenfang Cheng, Ling Yuan, Lin Ren, Changwei Pan, Irving R. Epstein, Qingyu Gao
Summary: In this study, the role of fast and slow inhibitors in oscillatory reaction networks was experimentally and theoretically analyzed. It was found that these inhibitors generate time delays and result in different oscillation patterns. This understanding is significant for the study of chemical and biochemical rhythms and the design of similar behaviors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Peripheral Vascular Disease
Jing Liu, Yong Liu, Feng Wang, Mingyu Liang
Summary: miR-204 is a high-value microRNA that plays a critical role in regulating cardiovascular and renal physiology, exhibiting tissue-specific expression patterns and being influenced by multiple regulatory mechanisms. It attenuates pulmonary arterial hypertension and renal injury while promoting hypertension and endothelial dysfunction, potentially impacting disease processes through targeting various biological pathways. Dysregulation of miR-204 in cardiovascular and renal diseases highlights its unequivocal functional roles and clinical relevance.
Article
Biotechnology & Applied Microbiology
Derrick Shih-Wei Chuang, James C. Liao
Summary: This study revealed the important role of phosphoketolase (Xpk) in primary metabolism of cyanobacteria, particularly in energy regulation and dark conditions. Additionally, Xpk is involved in the pathway producing ATP from glycogen to acetate. Deletion of xpk leads to glucose secretion under dark, anaerobic conditions.
METABOLIC ENGINEERING
(2021)
Review
Biochemistry & Molecular Biology
Agnieszka Chelkowska-Pauszek, Jan Grzegorz Kosinski, Klementyna Marciniak, Marta Wysocka, Kamilla Bakowska-Zywicka, Marek Zywicki
Summary: Bacteria have developed mechanisms for immediate adjustment of gene expression in response to changing environmental conditions, often relying on RNA-dependent regulatory mechanisms. The high dynamics and flexibility of RNA structure provide the necessary sensitivity and specificity for efficient sensing and transduction of environmental signals. This review discusses bacterial regulatory mechanisms based on RNA structure and presents examples of RNA regulators' multiple mechanisms in controlling bacterial transcription and translation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Amelie Vergnol, Massire Traore, France Pietri-Rouxel, Sestina Falcone
Summary: Voltage-gated calcium channels play crucial roles in regulating intracellular calcium levels and influencing various physiological processes in cells. The auxiliary CaV beta subunits, particularly their involvement in modulating Ca2+ signaling and gene expression, have been highlighted in recent research findings.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Aishwarya Gurumurthy, David T. Yu, Jared R. Stees, Pamela Chamales, Ekaterina Gavrilova, Paul Wassel, Lu Li, Daniel Stribling, Jinyang Chen, Marissa Brackett, Alexander M. Ishov, Mingyi Xie, Jorg Bungert
Summary: SEs mediate high transcription levels by recruiting transcription complexes and generating eRNAs. The LCR is able to recruit transcription complexes independently from linked genes, and HS2 initiates bidirectional transcription. Integrator complex plays a role in terminating eRNA transcription and interacts downstream of LCR HS2, affecting transcription of beta-globin genes.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biology
Arsala Ali, Kyudong Han, Ping Liang
Summary: Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of genomes, contributing to gene regulation by providing cis-regulatory sequences and encoding regulatory RNAs. These TE-derived regulatory mechanisms play crucial roles in gene regulation, providing evolutionary novelty and tissue-specific functions.
Review
Engineering, Chemical
Hyeseon Jeong, Kyung Hwan Park, Yuri Lee, Ayoung Jeong, Sooji Choi, Kyung Won Kim
Summary: PIWI proteins and piRNAs play roles in regulating upstream or downstream oncogenes or tumor-suppressor genes in cancer tissues, which may have potential applications in cancer therapeutics and as cancer biomarkers, indicating their important research significance.
Article
Biochemistry & Molecular Biology
Yuntian Ye, Yongqiang Liu, Xiaolong Li, Guangyi Wang, Quan Zhou, Qing Chen, Jiale Li, Xiaorong Wang, Haoru Tang
Summary: This study identified BBX transcription factors in cultivated and wild strawberries, revealing the expansion of gene family is related to whole-genome or segmental duplication. Loss and acquisition events of FaBBX genes might affect agronomic traits, and some FaBBX genes showed changes in transcriptional activity in response to blue light treatment. FaBBX28c1, in particular, could play a crucial role in flowering time regulation in cultivated strawberry.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Fen Feng, Peng Jiao, Jinpeng Wang, Yanxia Li, Binwu Bao, Zhuoma Luoreng, Xingping Wang
Summary: This article summarizes the regulatory role of lncRNAs in immune responses and their association with various diseases, providing references for the molecular regulation, genetic diagnosis, and treatment of inflammatory diseases.
Article
Multidisciplinary Sciences
Qi-Ming Chen, Michael Fischer, Yuki Nojiri, Michael Renger, Edwar Xie, Matti Partanen, Stefan Pogorzalek, Kirill G. Fedorov, Achim Marx, Frank Deppe, Rudolf Gross
Summary: By measuring the non-equilibrium dynamics of a superconducting Duffing oscillator, we experimentally reconcile the classical and quantum descriptions and explain the classically regarded steady states as quantum metastable states. Our results reveal a smooth quantum state evolution behind a sudden dissipative phase transition and provide insights into the intriguing phenomena in driven-dissipative systems.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Shizhou Wu, Junqi Zhang, Qi Peng, Yunjie Liu, Lei Lei, Hui Zhang
Summary: Antibiotic resistance, particularly in MRSA infections, is a serious global health concern with significant social and financial consequences. The YycFG two-component signal transduction system in Staphylococcus aureus is crucial for bacterial viability and plays a key role in cell membrane metabolism, cell wall synthesis, and biofilm formation. Inhibition of the YycFG pathway shows promise as a potential target for managing MRSA-induced infections by reducing biofilm formation and bacterial pathogenicity.
Article
Mathematics, Applied
Ll Alseda, B. Vidiella, R. Sole, J. T. Lazaro, J. Sardanyes
COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION
(2020)
Article
Biochemical Research Methods
Salva Duran-Nebreda, Jordi Pla, Blai Vidiella, Jordi Pinero, Nuria Conde-Pueyo, Ricard Sole
Summary: This article discusses the characteristics of multicellular entities and their spatial patterns related to functions, as well as the repeating distributions in biological structures. It introduces patterning modules and synthetic gene circuits, along with the phenomenon of symmetry-breaking demonstrated through experimental results.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biology
Ricard Sole, Guim Aguade-Gorgorio
Summary: Differentiation therapy (DTH) is a promising approach to cancer treatment, showing success in specific types of cancer. Mathematical framework and ecological models provide insights for therapy design, but challenges remain in its application to solid tumors.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Green & Sustainable Science & Technology
Josep M. Anto, Jose Luis Marti, Jaume Casals, Paul Bou-Habib, Paula Casal, Marc Fleurbaey, Howard Frumkin, Manel Jimenez-Morales, Jacint Jordana, Carla Lancelotti, Humberto Llavador, Lela Melon, Ricard Sole, Francesc Subirada, Andrew Williams
Summary: We are living in a time that requires massive and novel coordinated scientific and societal efforts to address pressing challenges threatening catastrophic change to the natural environment. Universities and academic institutions have the opportunity and responsibility to take a leading role in this era. The Planetary Wellbeing Initiative aims to promote the highest attainable standard of wellbeing for both human and non-human beings, requiring collaboration across various fields to tackle the challenges of global complexity, interdisciplinarity, and urgency.
Article
Respiratory System
Martin L. Watzenboeck, Anna-Dorothea Gorki, Federica Quattrone, Riem Gawish, Stefan Schwarz, Christopher Lambers, Peter Jaksch, Karin Lakovits, Sophie Zahalka, Nina Rahimi, Philipp Starkl, Doerte Symmank, Tyler Artner, Celine Pattaroni, Nikolaus Fortelny, Kristaps Klavins, Florian Frommlet, Benjamin J. Marsland, Konrad Hoetzenecker, Stefanie Widder, Sylvia Knapp
Summary: Lung transplantation is the ultimate treatment option for patients with end-stage respiratory diseases, but the mortality rate is high due to chronic lung allograft dysfunction (CLAD). The mechanisms leading to CLAD are not well understood due to insufficient understanding of post-transplant adaptation processes. This study analyzed bronchoalveolar lavage samples from lung recipients and donors, and found that recipient-specific and environmental factors shape the long-term lung microbiome. Certain bacterial strains were found to be correlated with underlying lung diseases even after transplantation. Machine learning techniques accurately predicted future changes in lung function, with the microbial profiles showing high predictive power. The study highlights the importance of understanding lung adaptation processes and the role of microbiome in predicting allograft function.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Blai Vidiella, Antoni Guillamon, Josep Sardanyes, Victor Maull, Jordi Pla, Nuria Conde, Ricard Sole
Summary: This paper presents an engineered gene network that displays self-organized criticality (SOC) behavior in living cells, poising them close to a critical state. The authors discuss the potential implications of this state on cellular dynamics and behavior.
NATURE COMMUNICATIONS
(2021)
Correction
Multidisciplinary Sciences
Blai Vidiella, Antoni Guillamon, Josep Sardanyes, Victor Maull, Jordi Pla, Nuria Conde, Ricard Sole
NATURE COMMUNICATIONS
(2021)
Article
Biology
Guim Aguade-Gorgorio, Stuart Kauffman, Ricard Sole
Summary: Phenotypic switching in cancer cells is a common phenomenon across tumor types and plays a crucial role in tumor evolution and therapy resistance. A mathematical framework has been developed to understand the dynamics of phenotypic switching, which provides insights for the success of combination therapies targeting both replication and phenotypic transitions.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Ecology
Miguel Berdugo, Blai Vidiella, Ricard V. Sole, Fernando T. Maestre
Summary: With ongoing climate change, the probability of exceeding aridity thresholds in drylands and experiencing abrupt ecosystem changes is higher than ever. By identifying different mechanisms causing aridity thresholds and potential amplification mechanisms, we can develop specific hypotheses to bridge knowledge gaps and focus on monitoring and adapting to abrupt ecosystem changes in global drylands.
FUNCTIONAL ECOLOGY
(2022)
Article
Ecology
Stefanie Widder, Jiangchao Zhao, Lisa A. Carmody, Qingyang Zhang, Linda M. Kalikin, Patrick D. Schloss, John J. LiPuma
Summary: In this study, bacterial communities in the airways of cystic fibrosis patients were analyzed, leading to the identification of different pulmotypes which show temporal sequence patterns and significant correlations with patient clinical status. By constructing pulmotype-specific metabolic activity profiles, it was found that microbial communities within pulmotypes drive distinct community functions.
Review
Physics, Multidisciplinary
Ricard Sole, Josep Sardanyes, Santiago F. Elena
Summary: Viruses have complex relationships with other organisms, sometimes parasitizing them and causing diseases, while also playing a pivotal role in the evolution of their hosts.
REPORTS ON PROGRESS IN PHYSICS
(2021)
Article
Ecology
Patrick Fraser, Ricard Sole, Gemma de las Cuevas
Summary: The article discusses why the brain can understand self-reference and introduces the "Strange Loop Model" to explain this phenomenon. This model involves causal feedback between two brain modules to avoid paradoxes of self-reference and negation. It also suggests that the brain's metastable dynamics can limit endless reasoning. Finally, the representation of logical inconsistencies in the model leads to causal incongruence between brain subsystems.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Stefanie Widder, Irene Goerzer, Benjamin Friedel, Nina Rahimi, Stefan Schwarz, Peter Jaksch, Sylvia Knapp, Elisabeth Puchhammer-Stoeckl
Summary: This study provides a detailed analysis of virome dynamics after lung transplantation, revealing host, body compartment, and time-specific dependency patterns among viruses. The results also suggest genetic adaptation to the host microenvironment at the level of the virome and support the hypothesis of functional complementarity between Anellovirus groups and other persistent viruses.
Correction
Microbiology
Stefanie Widder, Irene Goerzer, Benjamin Friedel, Nina Rahimi, Stefan Schwarz, Peter Jaksch, Sylvia Knapp, Elisabeth Puchhammer-Stoeckl
Meeting Abstract
Cardiac & Cardiovascular Systems
S. Widder, R. Gawish, M. Watzenboeck, A. Gorki, F. Quattrone, S. Schwarz, C. Lambers, P. Jaksch, K. Lakovits, S. Zahalka, N. Rahimi, P. Starkl, D. Symmank, T. Artner, K. Hoetzenecker, S. Knapp
JOURNAL OF HEART AND LUNG TRANSPLANTATION
(2021)
