Article
Chemistry, Physical
Palash Bera, Abdul Wasim, Pushpita Ghosh
Summary: Reproducing bacteria can self-organize to form patterned biofilms in various conditions. The aggregation and phase separation of bacteria are influenced by motility force and self-secreted extracellular polymeric substances (EPS) under far-from-equilibrium conditions. Increased motility force hinders depletion-induced cell aggregation and phase segregation, requiring a higher depletion effect for highly motile bacteria to undergo phase separation. Additionally, clustering dynamics and differential dispersion among components can also affect the morphology of a developing colony.
Article
Environmental Sciences
Wen-Jie Ma, Jiang-Tao Zhang, Ye Wang, Gui-Feng Li, Xin-Xin Wu, Yu-Xi Yao, Ya-Fei Cheng, Bao-Cheng Huang, Ren-Cun Jin
Summary: Arsenic has a negative impact on anammox treatment technology, while extracellular polymeric substances (EPS) play an important role in resisting this toxicity. In this study, it was found that proteins are the main component in EPS that forms complexes with arsenic, and complexation and hydrophobic interactions are the main forces preventing arsenic invasion.
Article
Environmental Sciences
Xinyue Lu, Wenjie Xu, Caixia Liu, Quanlin Zhao, Zhengfang Ye
Summary: EPS plays a significant role in nitrobenzene treatment, acting as both a reservoir for nitrobenzene and a protector of cells from toxicity. EPS helps maintain the stability of microbial communities by alleviating the negative impacts of nitrobenzene on inner cells.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Environmental Sciences
Mai Liu, Peipei Meng, Guichang Chen, Ying Guan, Guoqiang Liu
Summary: This study investigated the correlation between structural extracellular polymeric substances and solids retention time and biofilm structures in a dynamic membrane bioreactor. The results showed that alginate-like extracellular polysaccharide was negatively correlated to biofilm hydraulic resistance, while amyloid-like protein was positively correlated to biofilm hydraulic resistance.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Physical
Nestor M. de los Santos-Lopez, Gabriel Perez-Angel, Jose M. Mendez-Alcaraz, Ramon Castaneda-Priego
Summary: The article systematically studies the depletion interactions between colloidal particles, focusing on how the composition of depletants drives the competition between attraction and repulsion. Results are obtained through theoretical analysis and computer simulations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Palash Bera, Abdul Wasim, Pushpita Ghosh
Summary: This study investigates the role of motility force and self-secreted extracellular polymeric substances (EPS) in bacterial cell aggregation and phase separation. The findings show that increased motility force hinders cell aggregation and phase segregation, requiring a higher depletion effect for highly motile bacteria to undergo phase separation. The study also reveals the dynamic nature of clustering and the localization of EPS at the periphery of a growing colony.
Article
Environmental Sciences
Jayesh M. Sonawane, Ashutosh Kumar Rai, Minaxi Sharma, Manikant Tripathi, Ram Prasad
Summary: Microbial biofilms, formed through the adherence of bacteria via polymer matrices, play a significant role in the bioremediation of organic pollutants. Tuning parameters such as quorum sensing and adhesion surface characteristics can enhance the effectiveness of biofilm-based bioremediation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Xianxin Luo, Xiaoyu Zhou, Chengyi Peng, Penghui Shao, Feng Wei, Shujing Li, Ting Liu, Liming Yang, Lin Ding, Xubiao Luo
Summary: This study found that extracellular polymeric substances (EPS) play an important role in reducing hexavalent chromium, shedding light on the mechanisms of EPS. The researchers discovered that adding EPS and tryptophan significantly improved the reduction efficiency of hexavalent chromium. These findings provide new insights and strategies for removing heavy metal contamination in future applications.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Chemistry, Inorganic & Nuclear
Tomoya Iizuka, Nobuhiko Hosono, Takashi Uemura
Summary: In this study, the mechanical properties of metal-organic frameworks (MOFs) are improved by filling the MOF pores with polymer chains, resulting in enhanced resilience and toughness against mechanical pressures.
DALTON TRANSACTIONS
(2022)
Article
Environmental Sciences
Gui-Feng Li, Zhi-Qi Ren, Ye Wang, Jing-Peng Li, Wen-Jie Ma, Ya-Fei Cheng, Bao-Cheng Huang, Ren-Cun Jin
Summary: This study explored the interaction between phenol and EPSs as well as the Amt domain at the molecular level. The results showed that EPSs played a protective role in preventing phenol toxicity, while the interaction between phenol and the Amt domain affected the activity of Anammox sludge.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Yanni Xi, Tanghuan Xie, Yanfen Liu, Yangtao Wu, Huinian Liu, Zhu Su, Yicai Huang, Xingzhong Yuan, Chang Zhang, Xin Li
Summary: The composite material CMC-FeS@EPS was developed for the removal of Cr(VI) from water, showing higher efficiency compared to traditional materials, with good performance in a wide range of pH values and in the presence of other ions. FTIR and XPS analysis demonstrated that EPS functional groups accelerated the adsorption and precipitation process, while electrochemical results showed faster electron transfer to Cr(VI) in CMC-FeS@EPS compared to CMC-FeS.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Hui An, Tian Tian, Ziting Wang, Ruofei Jin, Jiti Zhou
Summary: Microbial remediation is a promising approach for managing and restoring heavy metal-contaminated soils. This study investigated the immobilization of Cr(VI) by Shewanella putrefaciens CN32 unsaturated biofilms and explored the underlying mechanisms of Cr(VI) complexation. The results showed that Cr(VI) had a dose-dependent toxicity to the growth of unsaturated biofilms. The extracellular polymeric substances (EPS) were found to be the primary components for Cr(VI) immobilization, accounting for over 60% of the total adsorbed Cr(VI). The study also revealed that hydroxyl, carboxyl, phosphoryl, and amino functional groups in proteins and polysaccharides of EPS were the binding sites for immobilizing Cr(VI). Starved unsaturated biofilms released the EPS-bound Cr(VI) due to the depletion of EPS, which further aggravated the toxicity of Cr(VI) to the cells. This study expands our understanding of Cr(VI) immobilization by unsaturated biofilms and provides valuable information for the remediation of heavy metal-contaminated soils.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Polymer Science
Yongchuan Wu, Wenqian Xing, Jing Wen, Zhonglian Wu, Ya Zhang, Hechuan Zhang, Haidi Wu, Hang Yao, Huaiguo Xue, Jiefeng Gao
Summary: We report a facile one-step mixed solvent-exchange strategy to prepare high-performance organohydrogels (or organogels) with abundant hydrogen bonds, entanglements, and crystalline domains. These gels exhibit excellent mechanical properties including high strength (up to 8.39 +/- 0.51 MPa), fracture strain (up to 1127 +/- 123%), toughness (52.63 +/- 1.98 MJ/m(3)), fracture energy (up to 16.34 +/- 5.6 kJ m(-2)), anti-freezing (-65 degrees C), long-term tolerance (95% of retention coefficient for 14 d), thermal stability (110 degrees C), transparency (over 90%), and biocompatibility.
Article
Polymer Science
Sergei A. A. Egorov
Summary: The study utilized Density Functional Theory to investigate depletion interactions between nanoparticles mediated by semiflexible polymers, revealing that the depletion attraction becomes stronger with increasing polymer chain stiffness and colloidal particle size.
Review
Environmental Sciences
T. Siddharth, P. Sridhar, V. Vinila, R. D. Tyagi
Summary: EPS, as a potential bioflocculant, possesses numerous advantages such as renewability, biodegradability, eco-friendliness, non-toxicity, and economic value. It can be used as an adsorbent for removing dyes and heavy metals from industrial effluents, as well as for soil remediation and erosion control.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Biochemistry & Molecular Biology
Veronika te Boekhorst, Liying Jiang, Marius Mahlen, Maaike Meerlo, Gina Dunkel, Franziska C. Durst, Yanjun Yang, Herbert Levine, Boudewijn M. T. Burgering, Peter Friedl
Summary: This article studies the molecular mechanisms of cancer cell invasion and metastasis under hypoxic conditions and identifies calpain-2 as a key regulator of the transition from collective to amoeboid dissemination in breast and head and neck carcinoma cells. The study reveals that hypoxia induces calpain-2-mediated amoeboid conversion by deactivating beta 1 integrins. Targeted intervention of calpain-2 activity can restore normal cell phenotype and prevent lung metastasis.
Article
Biochemistry & Molecular Biology
Shubham Tripathi, Sumitabha Brahmachari, Jose N. Onuchic, Herbert Levine
Summary: Multiple RNA polymerases (RNAPs) transcribing a gene can exhibit collective behavior, where the transcription elongation rate increases with the rate of transcription initiation. Recent studies suggest that even RNAPs separated by long distances can cooperate by modifying the DNA segment under transcription. This theoretical model incorporates the mechanical coupling between RNAP translocation and DNA torsional response, and stochastic simulations demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Shubham Tripathi, Jun Hyoung Park, Shivanand Pudakalakatti, Pratip K. Bhattacharya, Benny Abraham Kaipparettu, Herbert Levine
Summary: Recent studies have shown that tumor cell metabolism is characterized by metabolic heterogeneity and plasticity. However, the field lacks a framework to analyze this heterogeneity and plasticity. Using a mechanistic model, researchers found that excess cytoplasmic ATP can drive a preference for aerobic glycolysis in fast-proliferating tumor cells, and the relative availability of glucose and glutamine can further drive metabolic heterogeneity. Additionally, the model can predict the metabolic and gene expression changes in cancer cells in response to drug treatment.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Cell Biology
Wen Jia, Mohit Kumar Jolly, Herbert Levine
Summary: The epithelial-mesenchymal transition (EMT) is a crucial cellular process for wound healing, cancer metastasis, and embryonic development. Recent studies have shown that hybrid epithelial/mesenchymal states, possessing both epithelial and mesenchymal traits, play a significant role in cancer metastasis and resistance to therapies. NRF2 has been identified as a stabilizing factor for these hybrid states. This research incorporates a phenomenological epigenetic feedback effect into a computational model for EMT signaling and demonstrates its stabilizing effect on the hybrid state if NRF2 influences SNAIL at an epigenetic level.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Srinath Muralidharan, Sarthak Sahoo, Aryamaan Saha, Sanjay Chandran, Sauma Suvra Majumdar, Susmita Mandal, Herbert Levine, Mohit Kumar Jolly
Summary: Research analysis reveals diverse associations between cancer cells' EMT status and metabolic pathways, showing that EMT is generally positively correlated with glycolysis but negatively correlated with oxidative phosphorylation and fatty acid metabolism. Additionally, higher levels of EMT and glycolysis predict a worse prognosis in many cancers.
Editorial Material
Multidisciplinary Sciences
Herbert Levine
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Samuel A. Vilchez Mercedes, Federico Bocci, Mona Ahmed, Ian Eder, Ninghao Zhu, Herbert Levine, Jose N. Onuchic, Mohit Kumar Jolly, Pak Kin Wong
Summary: In this study, the researchers used a combination of immunocytochemistry, single cell biosensors, and computational modeling to show that the transcription factor Nrf2 functions as a phenotypic stability factor for hybrid epithelial/mesenchymal cells during collective cancer migration. They also demonstrated that Nrf2 and EMT signaling are spatially coordinated near the leading edge, and that the Nrf2-EMT-Notch network enhances the expression of certain genes associated with the formation of leader cells and protruding tips.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Wen Jia, Atchuta Srinivas Duddu, Mohit Kumar Jolly, Herbert Levine
Summary: Biological cells can have different phenotypes determined by genetic networks, and the creation of landscapes is a popular way to represent these states. It is commonly believed that the landscape provides direct information about the state-to-state transition rates. However, this study shows that there is no direct correlation between the properties of the landscape and the corresponding transition rates.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Physics, Multidisciplinary
David A. Kessler, Herbert Levine
Summary: Drug persistence is an important phenomenon in cancer treatment, and finding effective strategies to eliminate persister cells is crucial.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
M. Ali Al-Radhawi, Shubham Tripathi, Yun Zhang, Eduardo D. Sontag, Herbert Levine
Summary: In this paper, the authors investigate the complex interactions between epigenetic marks, external signals, and gene-regulatory elements that lead to the emergence and transitions between distinct phenotypes in isogenic cells. They propose a mathematical modeling framework that considers both local and global competition effects between antagonistic epigenetic regulators, as well as the influence of local transcription factors. Applying this approach to experimental findings on the epithelial-mesenchymal transition, they are able to explain the observed data and provide verifiable predictions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Shubham Tripathi, David A. Kessler, Herbert Levine
Summary: Regulatory network models have proven to be effective tools for understanding and predicting cell-fate choice. This study shows that minimally frustrated networks can exhibit simple, low-dimensional steady-state behavior even in large and complex networks. These findings provide a theoretical explanation for the success of network models in biology and the challenges in network inference.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Paras Jain, Sophia Corbo, Kulsoom Mohammad, Sarthak Sahoo, Santhalakshmi Ranganathan, Jason T. George, Herbert Levine, Joseph Taube, Michael Toneff, Mohit Kumar Jolly
Summary: Epithelial-mesenchymal transition (EMT) and its reverse mesenchymal-epithelial transition (MET) play crucial roles in embryonic development, wound healing, and cancer metastasis. While short-term EMT induction can lead to reversible phenotypic changes, long-term EMT induction is often associated with irreversibility. In this study, we demonstrate that the phenotypic changes observed in MCF10A cells during long-term EMT induction by TGF-beta can in fact have longer timescales of reversibility. We also propose a mathematical model that explains how the epigenetic memory gained during long-term EMT induction can slow down the recovery to the epithelial state after TGF-beta withdrawal.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Physics, Fluids & Plasmas
Kevin Ng Chau, Jason T. George, Jose N. Onuchic, Xingcheng Lin, Herbert Levine
Summary: An affinity-based model for TCR-pMHC binding was studied, showing that the binding energy distribution depends on the number of contacts and the topology of the contact map. It was also quantified how neoantigens with mutations in sites with higher contacts are recognized at a higher rate.
Article
Physics, Multidisciplinary
Pedram Esfahani, Herbert Levine, Mrinmoy Mukherjee, Bo Sun
Summary: Directed cell migration is crucial in various physiological and pathophysiological processes. This study investigates the migration of breast cancer cells in the presence of both contact guidance and a chemoattractant gradient. The results reveal that the microstructure of the extracellular matrix plays a complex role in cell chemotaxis. Coherent extracellular matrix fibers significantly enhance chemotaxis efficiency when contact guidance is parallel to the chemical gradient, while cells exploit ECM disorder to locate paths for chemotaxis when contact guidance is perpendicular to the chemical gradient.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Oncology
Hiroko Masuda, Kenichi Harano, Sakiko Miura, Ying Wang, Yuko Hirota, Oi Harada, Mohit Kumar Jolly, Yuki Matsunaga, Bora Lim, Anita L. Wood, Napa Parinyanitikul, Hee Jin Lee, Gyungyub Gong, Jason T. George, Herbert Levine, Jangsoon Lee, Xiaoping Wang, Anthony Lucci, Arvind Rao, Brock L. Schweitzer, O. Rayne Lawrence, Robert S. Seitz, Stephan W. Morris, David R. Hout, Seigo Nakamura, Savitri Krishnamurthy, Naoto T. Ueno
Summary: The study found that TNBC molecular subtype and IM signature frequently change after NST, and the results suggest that EMT is promoted in the changed subtypes.
JCO PRECISION ONCOLOGY
(2022)