Article
Multidisciplinary Sciences
Michal Levo, Joao Raimundo, Xin Yang Bing, Zachary Sisco, Philippe J. Batut, Sergey Ryabichko, Thomas Gregor, Michael S. Levine
Summary: The prevailing view of metazoan gene regulation is challenged by recent findings that reveal physical and functional connections between genes separated by large genomic distances, providing new insights into gene regulation mechanisms.
Article
Mathematics, Interdisciplinary Applications
Changyan Di, Qingguo Zhou, Jun Shen, Jinqiang Wang, Rui Zhou, Tianyi Wang
Summary: The emergence of cooperation is a crucial issue in understanding collective behavior and evolution. Previous theoretical studies have observed periodic oscillations between cooperative and defective actions, but they do not fundamentally explain how cooperation emerges. This paper highlights the importance of considering inherent human memory characteristics in understanding this issue. By refining the eco-evolutionary game model using reinforcement learning, the authors show that oscillations between collective cooperation and defection can still occur, even if defection remains a strict Nash equilibrium.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Multidisciplinary Sciences
Jan J. Kreider, Thijs Janzen, Abel Bernadou, Daniel Elsner, Boris H. Kramer, Franz J. Weissing
Summary: This article demonstrates through a theoretical model that division of labour can emerge spontaneously within a group of entirely identical individuals. The authors show that if returning foragers share part of their resources with other group members, division of labour will emerge spontaneously and nutritional differences between individuals can reinforce division of labour.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Joydev Hatai, Yigit Altay, Ankush Sood, Armin Kiani, Marcel J. Eleveld, Leila Motiei, David Margulies, Sijbren Otto
Summary: Self-replicating systems are crucial for the study of life synthesis and origin, but traditional monitoring methods have limitations in throughput and requirements. To address these issues, we have developed a fluorescent molecular probe capable of real-time monitoring of the replication process, discriminating different replicators based on their chemical composition. This technique significantly reduces analysis time and sample quantities, and opens doors for high-throughput experimentation in protocell environments.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Green & Sustainable Science & Technology
Pengfei Yang, Shuhan Ge, Zhiqiang Liu, Lin-Lan Zhuang, Weijiang Li, Chao Liu, Jian Zhang
Summary: This study proposed a coupling process between algal ponds (AP) and constructed wetlands (AP-CW) to enhance wastewater purification performance. The results showed that adding 10.6 mg/(L.d) microalgae into the CW achieved a TN removal of 90.3%, with 1 g microalgae promoting 0.291 g N removal in CW. The optimal parameters for AP-CW were determined as 5 d HRT of AP and 0.4% microalgae reuse rate, resulting in TN and TP removal of 94.18% and 85.80% respectively.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Plant Sciences
R. K. F. Unsworth, S. C. Rees, C. M. Bertelli, N. E. Esteban, E. J. Furness, B. Walter
Summary: To maximize the potential of seagrass as a nature-based solution, large-scale restoration is needed. This study investigated the success of planting seagrass seeds using various treatments. The results showed that the addition of nutrients to sediment can improve seagrass shoot emergence and growth. However, the study also highlighted the variability in planting methods and the need for further research in seagrass restoration.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biodiversity Conservation
Kai-Ming Sun, Cuiqiong Zhao, Qing Ju, Yulu Tian
Summary: This study found that marine biofilms selectively utilize different nutrients, and only ammonium induced significant NIFTs phenomenon. We observed a linear relationship between fluorescence changes during ammonium-induced NIFTs and ammonium concentrations, with a final concentration of 500 μM ammonium triggering the most significant fluorescence increase. Therefore, nutrient-limited marine biofilms have the potential to monitor ammonium disturbance in water.
ECOLOGICAL INDICATORS
(2023)
Article
Physics, Multidisciplinary
Rodrigo A. Thomas, Michal Parniak, Christoffer ostfeldt, Christoffer B. Moller, Christian Baerentsen, Yeghishe Tsaturyan, Albert Schliesser, Jurgen Appel, Emil Zeuthen, Eugene S. Polzik
Summary: The study successfully achieved entanglement between a millimeter-sized mechanical membrane oscillator and a collective atomic spin oscillator, demonstrating an Einstein-Podolsky-Rosen variance below the separability limit. Overcoming the disparity of hybrid systems and the vulnerability of quantum correlations allowed for the generation of macroscopic hybrid entanglement.
Article
Management
Herve Legenvre, Ari-Pekka Hameri
Summary: To improve supply chain performance, companies are exploring new pathways such as industry-wide data sharing initiatives. This paper aims to stimulate research by describing the benefits, obstacles, and the governance of supply chain data sharing.
INTERNATIONAL JOURNAL OF OPERATIONS & PRODUCTION MANAGEMENT
(2023)
Article
Microbiology
Wei Hong, Raphael Nyaruaba, Xiaohong Li, Huan Liu, Hang Yang, Hongping Wei
Summary: The study found that phage lysins against Staphylococcus aureus biofilm could bind rapidly and start destroying the biofilm in a longer time period when monitored in real-time. Analysis using SPR platform revealed different affinity constants for lysins, suggesting that both the catalytic domain (CD) and cell-wall binding domain (CBD) affect the activity of the lysins against S. aureus biofilm.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Engineering, Environmental
Rebecca J. Wicker, Ehsan Daneshvar, Ashok Kumar Gupta, Hocheol Song, Eakalak Khan, Amit Bhatnagar
Summary: In this study, a constructed photosynthetic consortium was investigated for its carbon capture and nutrient removal capabilities. The consortium showed efficient removal of inorganic and organic carbon species, but suboptimal removal of phosphate and total nitrogen. However, nitrite and ammonia were almost completely depleted, indicating successful nitrogen removal. Real-time monitoring of the consortium's biodiversity and biofilm formation provided valuable insights into nutrient and carbon flux. This study highlights the importance of cultivating biodiverse and adaptable consortia for industrial applications and the utility of real-time monitoring for optimal performance.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Alexey Tiranov, Vasiliki Angelopoulou, Bjorn Schrinski, Cornelis Jacobus van Diepen, Oliver August Dall Alba Sandberg, Ying Wang, Leonardo Midolo, Sven Scholz, Andreas Dirk Wieck, Arne Ludwig, Anders Sondberg Sorensen, Peter Lodahl
Summary: Photon emission is fundamental for light-matter interaction and photonic quantum science. This study demonstrates distant dipole-dipole radiative coupling in solid-state optical quantum emitters embedded in a nanophotonic waveguide. The collective response and emission dynamics can be controlled by proper excitation techniques. This work is a foundational step towards multiemitter applications for scalable quantum-information processing.
Article
Limnology
Jian Shen, Jiabi Du, Lisa Lucas
Summary: Simple mathematical models provide insight into the relationships between import, export, transport, and internal removal for nonconservative substances in an estuary. These models can assess the relative importance of physical and biochemical processes and provide accurate estimates in practical applications.
LIMNOLOGY AND OCEANOGRAPHY
(2022)
Article
Business
Ling Ding, Juan Feng, Xiuwu Liao, Lu Yang
Summary: This study examines the impact of person-to-person (P2P) sharing markets on manufacturer's pricing strategies, consumers' consumption time, consumer surplus, and social welfare. It finds that the existence of a sharing market may result in higher prices, and the improvement of consumer surplus, manufacturer's profit, and social welfare depends on transaction costs and the proportion of high-quality consumers.
INTERNATIONAL JOURNAL OF ELECTRONIC COMMERCE
(2022)
Article
Engineering, Biomedical
Xiaoxia Kang, Xiaoxiao Yang, Conglin Guo, Yuechen Li, Haiwei Ji, Yuling Qin, Li Wu
Summary: Biofilms pose challenges in terms of bacterial characteristics and treatment, thus requiring the development of novel materials and strategies. This review provides a comprehensive summary of effective strategies and methodologies applicable across industries, including the process of biofilms formation, intervention strategies, treatment strategies, and antibacterial substances.
MATERIALS TODAY BIO
(2023)
Article
Clinical Neurology
Matteo Saponati, Jordi Garcia-Ojalvo, Enrico Cataldo, Alberto Mazzoni
Summary: In a feedforward network between the thalamus and primary sensory cortex, thalamic oscillations in the alpha range do not entrain cortical activity due to weaker oscillations in neurons projecting to the cortex and gamma resonance dynamics in the cortical networks hampering alpha range oscillations. This highlights the importance of corticothalamic feedback in sustaining alpha range oscillations for an integrated understanding of sensory stream transmission.
Article
Biochemistry & Molecular Biology
Kwang-Tao Chou, Dong-Yeon D. Lee, Jian-Geng Chiou, Leticia Galera-Laporta, San Ly, Jordi Garcia-Ojalvo, Gurol M. Suel
Summary: This study reveals a ring-like pattern in gene expression underlying the nitrogen stress response of a developing Bacillus subtilis biofilm. Mathematical modeling and experiments show that this pattern is generated by a clock and wavefront mechanism. The study also confirms that this mechanism is driven by cell-autonomous oscillations and is responsible for spatial patterning of sporulation within the biofilm.
Article
Multidisciplinary Sciences
Ronghui Zhu, Jesus M. del Rio-Salgado, Jordi Garcia-Ojalvo, Michael B. Elowitz
Summary: This study explores synthetic circuits that generate multiple stable states, providing insights into natural cell fate control circuit structures and enabling engineering of multicellular programs requiring interactions among distinct cell types.
Editorial Material
Biochemistry & Molecular Biology
Jordi Garcia-Ojalvo
Summary: This is a snapshot of the peer review process for a study on a synthetic gene circuit for imaging-free detection of signaling pulses (Ravindran et al., 2022).
Article
Biochemistry & Molecular Biology
Xuejie Wang, Casilda Olveira, Rosa Giron, Marta Garcia-Clemente, Luis Maiz, Oriol Sibila, Rafael Golpe, Rosario Menendez, Juan Rodriguez-Lopez, Concepcion Prados, Miguel Angel Martinez-Garcia, Juan Luis Rodriguez, David de la Rosa, Liyun Qin, Xavier Duran, Jordi Garcia-Ojalvo, Esther Barreiro
Summary: This study investigated different phenotypic characteristics in bronchiectasis patients based on neutrophil counts through biostatistics analysis, identifying two distinct clinical phenotypes. Patients with neutrophil counts above a certain threshold exhibited more severe lung function impairment, poorer nutritional status, and higher systemic inflammation compared to those below the threshold. Cluster analysis of combined systemic and respiratory variables defined well-distinguished phenotypic profiles in bronchiectasis patients.
Article
Microbiology
Tianmin Wang, Ping Shen, Ruochen Chai, Yihui He, Jintao Liu
Summary: In this study, researchers developed a new method called miniBac-seq for constructing high-quality bacterial RNA-seq libraries with ultra-low amounts of RNA. The method is 100-fold lower than the current benchmark kit and reduces preparation cost significantly. By applying miniBac-seq, the researchers were able to profile the transcriptome of growth-arrested bacteria, providing insights into bacterial physiology and regulation in their native contexts.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Kaito Kikuchi, Leticia Galera-Laporta, Colleen Weatherwax, Jamie Y. Lam, Eun Chae Moon, Emmanuel A. Theodorakis, Jordi Garcia-Ojalvo, Gurol M. Suel
Summary: Despite their dormant state, bacterial spores are able to sense environmental signals through a preexisting electrochemical potential and integrate these signals over time, affecting their decision to exit dormancy.
Article
Biochemistry & Molecular Biology
Sheng Wang, Jordi Garcia-Ojalvo, Michael B. Elowitz
Summary: This article demonstrates that a single morphogen is sufficient to generate stable spatial patterns in multicellular development and identifies key factors for robust pattern formation.
Article
Biochemistry & Molecular Biology
Tianmin Wang, Ping Shen, Yihui He, Yuzhen Zhang, Jintao Liu
Summary: This study used RAINBOW-seq to profile the transcriptome of Escherichia coli biofilm communities and discovered three modes of community-level coordination. It also revealed that the nutrient-limited region of the community maintained a high level of metabolism and expressed various signaling genes and functionally unknown genes with potential sociality functions.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Rosa Martinez-Corral, Minhee Park, Kelly M. Biette, Dhana Friedrich, Clarissa Scholes, Ahmad S. Khalil, Jeremy Gunawardena, Angela H. DePace
Summary: Transcription factors (TFs) control gene expression by acting synergistically and recent research suggests that kinetic synergy can arise through TFs acting on distinct steps of the transcription cycle. In this study, a synthetic circuit was built to investigate the complex landscape of mRNA production dependent on TF concentration, DNA binding affinity, and regulatory activity. The results confirmed that the transcription cycle must be integrated with recruitment for a quantitative understanding of gene regulation.
Article
Cell Biology
Xue-Kun Guo, Jiali Wang, Vincent P. van Hensbergen, Jintao Liu, Huji Xu, Xiaoyu Hu
Summary: This study reveals a unique pattern of crypt occupation by mucus-associated biofilms during early colitis, which is genetically dependent on bacterial biofilm-forming capacity and restricted by host epithelial O 1,2-fucosylation. Deficiency in O 1,2-fucosylation leads to increased crypt occupation by biofilms and exacerbated intestinal inflammation. Mechanistically, fucose from biofilm-occupied mucus suppresses biofilm formation and related genes. Additionally, fucose administration ameliorates experimental colitis, suggesting the therapeutic potential of fucose for biofilm-related disorders.
Article
Computer Science, Cybernetics
Pau Clusella, Elif Koksal-Ersoz, Jordi Garcia-Ojalvo, Giulio Ruffini
Summary: Neural mass models (NMMs) aim to replicate the collective dynamics of neuronal populations. A common framework assumes that the firing rate of a population can be described by a static nonlinear transfer function. However, a recent theory challenges this view by showing that the firing rate follows nonlinear differential equations. This study analyzes and compares these two descriptions in the presence of second-order synaptic dynamics.
BIOLOGICAL CYBERNETICS
(2023)
Article
Clinical Neurology
Ruben Molina-Fernandez, Pol Picon-Pages, Alejandro Barranco-Almohalla, Giulia Crepin, Victor Herrera-Fernandez, Anna Garcia-Elias, Hugo Fanlo-Ucar, Xavier Fernandez-Busquets, Jordi Garcia-Ojalvo, Baldomero Oliva, Francisco J. Munoz
Summary: Alzheimer's disease and Type 2 diabetes are linked to aging, and there is a connection between Alzheimer's disease and insulin resistance. The aggregation of amyloid beta-peptide into beta-sheets is the main characteristic of Alzheimer's disease. In this study, it was found that monomeric amyloid beta-peptide 1-40 shares a similar structure to insulin and can activate insulin receptor. However, the accumulation and oligomerization of amyloid beta-peptide can block the insulin receptor, leading to insulin resistance and compromising neuronal metabolism and protective pathways.
BRAIN COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Yuzhen Zhang, Yumin Cai, Lingbin Zeng, Peng Liu, Luyan Z. Ma, Jintao Liu
Summary: This study presents a microfluidic approach for quantitatively measuring the spatial heterogeneity of bacterial biofilms and demonstrates its advantages through two examples on biofilm homeostasis and stress response.
Article
Biochemistry & Molecular Biology
Xuejie Wang, Carmen Villa, Yadira Dobarganes, Casilda Olveira, Rosa Giron, Marta Garcia-Clemente, Luis Maiz, Oriol Sibila, Rafael Golpe, Rosario Menendez, Juan Rodriguez-Lopez, Concepcion Prados, Miguel Angel Martinez-Garcia, Juan Luis Rodriguez, David de la Rosa, Xavier Duran, Jordi Garcia-Ojalvo, Esther Barreiro
Summary: Differential phenotypic clusters were identified in a large cohort of bronchiectasis patients using data mining approaches. The three clusters were classified as mild, moderate, and severe based on systemic biomarkers, with severe cluster exhibiting worse disease severity and poorer outcomes. Clustering analysis proved to be a powerful tool in characterizing the complexity and heterogeneity of bronchiectasis patients.
