Article
Biochemistry & Molecular Biology
Amy O. Stevens, Yi He
Summary: PICK1 is a multi-domain scaffolding protein containing both a PDZ domain and a BAR domain. Molecular dynamics simulations have revealed the internal regulation mechanisms, showing that interactions between the PDZ domain and the BAR domain are driven by hydrophobic forces. The simulations also demonstrate that the C-terminus interacts dynamically with the BAR domain through a combination of electrostatic and hydrophobic interactions.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Environmental Sciences
S. Junttila, T. Holtta, N. Saarinen, V. Kankare, T. Yrttimaa, J. Hyyppa, M. Vastaranta
Summary: The study investigated the use of novel small hyperspectral sensors for non-destructive estimation of leaf water content. Results showed that the sensors captured variations in equivalent water thickness and relative water content, providing detailed insights into the dynamics of leaf water content. The study concluded that close-range hyperspectral spectroscopy can be a novel tool for continuous measurement of leaf water content and better understanding of plant responses to environmental conditions.
REMOTE SENSING OF ENVIRONMENT
(2022)
Article
Chemistry, Physical
Li Xu, Jingyu Wang, Aiting Zhang, Yuxia Pang, Dongjie Yang, Hongming Lou, Xueqing Qiu
Summary: Quantitative analysis of the intermolecular forces between lignin and cellulases at different temperatures revealed that increasing temperature improves adsorption capacity and total intermolecular forces. Hydrophobic forces and van der Waals forces contribute to long-range attractions, while electrostatic forces exhibit repulsive effects. Short-range forces including hydrogen bonding and 7L-7L stacking stabilize the non-specific binding of enzymes to lignin. Increasing temperature reduces hydrogen bond number and increases the relative contribution of long-range forces. The study also highlights the importance of hydrophobic interactions, hydrogen bonding, and steric effects in driving adsorption capacity and glucose yields.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Physical
Ran Tivony, Yu Zhang, Jacob Klein
Summary: Experimental results reveal that frictional dissipation between metal and dielectric surfaces can significantly vary under different conditions, primarily affected by the potential applied to the metal. Under specific conditions, frictional dissipation is high with a high coefficient of friction, while under another condition, frictional dissipation is lower with a smaller coefficient of friction.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Biotechnology & Applied Microbiology
Veera Kainulainen, Carina Von Schantz-Fant, Ruusu-Maria Kovanen, Swapnil Potdar, Karoliina Laamanen, Jani Saarela, Reetta Satokari
Summary: In this study, a high-throughput screening assay was developed to explore the binding receptors of intestinal epithelial cells for Bifidobacterium bifidum. Four cell surface proteins, SERPINB3, LGICZ1, PKD1, and PAQR6, were identified as potential receptors. Blocking these host cell proteins significantly decreased the binding of B. bifidum to the intestinal cell lines. These proteins are involved in the regulation of cellular processes related to proliferation, differentiation, apoptosis, inflammation, and immunity, providing insights into the mechanisms of B. bifidum-host interactions and its regulation of intestinal homeostasis.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Nanoscience & Nanotechnology
Lei Xie, Xin Cui, Jing Liu, Qiuyi Lu, Jun Huang, Xiaohui Mao, Diling Yang, Jinglin Tan, Hao Zhang, Hongbo Zeng
Summary: The mussel-inspired polydopamine (PDA) can be deposited on various substrates and possess versatile wet adhesion, but its interaction with slippery surfaces remains unclear. Liquid-infused poly(tetrafluoroethylene) (LI-PTFE) and solid slippery surfaces were found to effectively prevent PDA deposition, with LI-PTFE demonstrating excellent antifouling and self-cleaning properties even when interacting with PDA wet adhesives.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Engineering, Environmental
Yong-Tao Lv, Xiaolin Chen, Xuyang Zhang, Yue Li, Qinghu Lv, Rui Miao, Lujie Nie, Lei Wang
Summary: In this study, denitrifying granular sludge was successfully cultivated under acidic pH conditions using a sequencing batch reactor. By increasing the content of extracellular polymeric substances (EPS), high activity and efficient nitrogen removal were achieved. The role of protein (PN) and exopolysaccharide (PS) in granule formation was investigated, with PN playing a dominant role.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Francisco J. Fernandez, Jorge Santos-Lopez, Ruben Martinez-Barricarte, Javier Querol-Garcia, Hector Martin-Merinero, Sergio Navas-Yuste, Martin Savko, William E. Shepard, Santiago Rodriguez de Cordoba, M. Cristina Vega
Summary: This study reveals the structural basis of the interaction between human opsonin iC3b and the von Willebrand A inserted domain of the alpha chain of CR3, providing insights into complement activation and pathogen clearance by macrophages.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Applied
Ayoub El Baraka, Anouar Jorio, Ahmed Ennaoui, Asmae Khaldoun
Summary: This paper provides an overview of the adhesion mechanism of dust on the surfaces of concentrated solar power mirrors and presents a facile method for assessing different types of anti-soiling coatings to improve the efficiency of solar plants.
JOURNAL OF COATINGS TECHNOLOGY AND RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Joanna Dziadkowiec, Matea Ban, Shaghayegh Javadi, Bjorn Jamtveit, Anja Royne
Summary: The study indicates that hydrated calcium ions decrease adhesion between calcite surfaces compared to monovalent sodium ions, which may sustain thick water films even at high overburden pressures, leading to a possible loss of cohesion for weakly charged minerals.
ACS EARTH AND SPACE CHEMISTRY
(2021)
Article
Gastroenterology & Hepatology
Munkhtsetseg Banzragch, Kemal Sanli, Christen Rune Stensvold, Ozgur Kurt, Sule Ari
Summary: The microbiota composition of colonic cleansing fluid (CCF) collected during colonoscopy has been found to distinguish patients with inflammatory bowel disease (IBD) from healthy controls, suggesting that CCF analysis can be an alternative strategy for early diagnosis and disease progression in IBD biomarker research.
SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Chemistry, Physical
A. A. Ganne
Summary: The macroscopic theory of van der Waals forces was employed to calculate the disjoining pressure isotherms for silicone oil and perfluorodecalin films on silica substrates. The analysis allowed estimation of the ranges of stable oil film thicknesses applicable as water-repellent slippery coatings.
Article
Engineering, Biomedical
Theresa C. Ezenwafor, Vanessa O. Uzonwanne, Jonathan U. A. Madukwe, Said M. Amin, Vitalis C. Anye, John D. Obayemi, Olushola S. Odusanya, Winston O. Soboyejo
Summary: This paper presents a combined experimental and theoretical study on the adhesion between molecular recognition units and receptors on tumor surfaces. The results show that the adhesion forces and energies between high-grade TNBC tissues and Luteinizing Hormone Releasing Hormone (LHRH) or Epherin type A2 (EphA2) are significantly higher than those with normal human breast tissues. These findings have important implications for the development of targeted nanostructures for the detection and treatment of TNBC.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2022)
Article
Chemistry, Physical
David H. Cho, Jong-in Hahm
Summary: With the advancement of nanoscience and nanotechnology, novel protein interaction phenomena driven by nanoscale polymer interfaces have been discovered. The use of single biomolecule level approaches provides direct experimental evidence of protein-polymer interactions and yields unique insights into the mechanisms and kinetics of these interactions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Microbiology
Sebastian Pfeilmeier, Gabriella C. Petti, Miriam Bortfeld-Miller, Benjamin Daniel, Christopher M. Field, Shinichi Sunagawa, Julia A. Vorholt
Summary: This study demonstrates that the maintenance of leaf microbiota homeostasis in Arabidopsis thaliana plants requires the involvement of the NADPH oxidase RBOHD, as its absence leads to enrichment of opportunistic pathogens. The composition of plant microbiota is greatly influenced by the plant immune system, highlighting the importance of both immune system and microbial community in maintaining plant health.
NATURE MICROBIOLOGY
(2021)
Article
Microbiology
Christine M. Vogel, Daniel B. Potthoff, Martin Schafer, Niculo Barandun, Julia A. Vorholt
Summary: Systematic analysis of bacterial isolates from the phyllosphere of Arabidopsis thaliana identified protective strains against the pathogen Pseudomonas syringae pv. tomato DC3000, demonstrating direct bacteria-pathogen interactions. While some strains confer full protection through pattern-triggered immunity, others protect independently of plant immunity receptors. The study highlights the importance of identifying key genes of the microbiota for plant protection.
NATURE MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Lucas Hemmerle, Benjamin A. Maier, Miriam Bortfeld-Miller, Birgitta Ryback, Christoph G. Gabelein, Martin Ackermann, Julia A. Vorholt
Summary: This study empirically tested the concept of dynamic character displacement among interacting bacterial species from leaf-colonizing families using a proteomics approach. The results revealed phenotypic shifts and reduced niche overlap during coexistence, indicating the importance of species differences in promoting stable coexistence. The study also demonstrated the relevance of phenotypic plasticity in mediating character displacement and facilitating species coexistence.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Christoph G. Gabelein, Qian Feng, Edin Sarajlic, Tomaso Zambelli, Orane Guillaume-Gentil, Benoit Kornmann, Julia A. Vorholt
Summary: The study developed a FluidFM-based approach that enables the manipulation of organelles within single live cells. It allows for the extraction, injection, and transplantation of organelles with subcellular spatial resolution. The transferred organelles, such as mitochondria, can fuse with the host cells' organelle network.
Article
Microbiology
Martin Schaefer, Christine M. Vogel, Miriam Bortfeld-Miller, Maximilian Mittelviefhaus, Julia A. Vorholt
Summary: This study investigates bacterial interactions in the phyllosphere microbiota using a synthetic community. The results show that 90% of the interactions in planta were negative and closely related strains had consistent effects on the synthetic community. The changes in the community could be largely explained by binary interactions, but higher-order interactions involving more than two strains were also identified.
NATURE MICROBIOLOGY
(2022)
Article
Biology
Orane Guillaume-Gentil, Christoph G. Gaebelein, Stefanie Schmieder, Vincent Martinez, Tomaso Zambelli, Markus Kuenzler, Julia A. Vorholt
Summary: Guillaume-Gentil et al. present a method that utilizes a modified AFM tip to selectively sample and inject into fungal cells of different morphology. The authors made extensive modifications on their existing system for mammalian cells to overcome challenges encountered when working on single fungal cells. They demonstrate the effectiveness of fluidic force microscopy in injecting solutions and extracting cytoplasmic fluid from individual fungal cells, providing new opportunities for manipulating and analyzing fungi.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Wanze Chen, Orane Guillaume-Gentil, Pernille Yde Rainer, Christoph G. Gaebelein, Wouter Saelens, Vincent Gardeux, Amanda Klaeger, Riccardo Dainese, Magda Zachara, Tomaso Zambelli, Julia A. Vorholt, Bart Deplancke
Summary: Live-seq is a novel single-cell transcriptomic profiling approach that preserves cell viability during RNA extraction, allowing for the correlation analysis between a cell's ground-state transcriptome and its downstream molecular or phenotypic behavior. It accurately stratifies diverse cell types and states without major cellular perturbations, and can be used to map a cell's trajectory and evaluate gene effects on cell phenotypes.
Article
Ecology
Birgitta Ryback, Miriam Bortfeld-Miller, Julia A. Vorholt
Summary: Auxotrophs are organisms that cannot synthesize all the essential metabolites and rely on others for their survival. In a study of bacteria isolated from Arabidopsis thaliana leaves, it was found that about half of the strains require biotin, niacin, pantothenate, and/or thiamine. These auxotrophic strains were able to store coenzymes and grow exponentially for a few generations without vitamin supplementation, with biotin showing the highest storage capacity. Co-culture experiments showed that auxotrophic strains had higher species richness when provided with external vitamins. The results suggest that auxotrophs can benefit from metabolic by-products beyond vitamins.
Article
Multidisciplinary Sciences
Philipp Keller, Michael A. Reiter, Patrick Kiefer, Thomas Gassler, Lucas Hemmerle, Philipp Christen, Elad Noor, Julia A. Vorholt
Summary: This study reports the conversion of Escherichia coli into a synthetic methylotroph that can assimilate methanol via the ribulose monophosphate cycle. The methylotrophic E. coli strain optimizes methanol oxidation by upregulating an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway, and downregulating tricarboxylic acid cycle enzymes. This research lays the foundation for the efficient utilization of methanol as a carbon and energy resource.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Christoph G. Gaebelein, Michael A. Reiter, Chantal Ernst, Gabriel H. Giger, Julia A. Vorholt
Summary: Studying endosymbiosis is crucial for understanding cellular evolution and engineering. By injecting different bacteria into mammalian cells, we tested their potential for endosymbiosis and found that limiting the uptake of specific nutrients can slow down the intracellular growth of the endosymbiont.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Martin Schafer, Alan R. Pacheco, Rahel Kunzler, Miriam Bortfeld-Miller, Christopher M. Field, Evangelia Vayena, Vassily Hatzimanikatis, Julia A. Vorholt
Summary: Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria. The models recapitulated outcomes observed in planta with >89% accuracy, highlighting the role of carbon utilization and the contributions of niche partitioning and cross-feeding in the assembly of leaf microbiomes.
Article
Multidisciplinary Sciences
Julien Massoni, Miriam Bortfeld-Miller, Alex Widmer, Julia A. Vorholt
Summary: The study revealed that at least 25% of phyllosphere bacteria reach plants from the soil, with a majority belonging to the Burkholderiaceae family. These findings support future investigations on the routes used by soil microbes to reach leaves and flowers, as well as the ubiquitous environmental filtering of Burkholderiaceae across plant species and environments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Jethro L. Hemmann, Manuel R. Bruehwiler, Miriam Bortfeld-Miller, Julia A. Vorholt
Summary: Through high-resolution liquid chromatography-mass spectrometry, it was found that nine bacterial strains contained MYFR, with two strains resembling MYFR in M. extorquens and six strains containing modified MYFR. Gene deletions identified orf5, orfY, and orf17 as essential for MYFR biosynthesis, with Orf5 (now MyfB) playing a key role in glutamate addition. The study sheds light on the structural and functional features of MYFR biosynthesis in various bacterial strains.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Microbiology
Viktoriya Shyp, Badri Nath Dubey, Raphael Bohm, Johannes Hartl, Jutta Nesper, Julia A. Vorholt, Sebastian Hiller, Tilman Schirmer, Urs Jenal
Summary: This study demonstrates that the small signaling molecules (p)ppGpp and c-di-GMP reciprocally regulate the growth of Caulobacter crescentus by converging on the small-molecule-binding protein SmbA. (p)ppGpp promotes growth on glucose, while c-di-GMP inhibits glucose consumption, with SmbA playing a role in this metabolic switch and quenching redox stress associated with growth on glucose. The identification of SmbA as a central regulatory hub for these two global second messengers suggests potential for future studies on specific crosstalk between small-molecule-based regulatory networks.
NATURE MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Christoph G. Gaebelein, Michael A. Reiter, Chantal Ernst, Gabriel H. Giger, Julia A. Vorholt
Summary: Researchers tested the potential of artificial endosymbiosis in mammalian cells, and found that the growth rate of E. coli within the cell can be slowed down by limiting the uptake of aromatic amino acids, prolonging the survival of the endosymbiont-host pair.
ACS SYNTHETIC BIOLOGY
(2022)