Article
Multidisciplinary Sciences
Raushan Nugmanova, Yerlan Ramankulov, Pavel Tarlykov
Summary: The nonrandom distribution of mutations in a genome is a common phenomenon observed across different biological systems. This study demonstrates the presence of mutation clusters in the Gram-positive bacterium Bacillus subtilis, suggesting the universality of this phenomenon. The use of whole-genome sequencing proves to be an effective approach in studying mutation clusters.
Article
Biochemistry & Molecular Biology
Yun-Lu Sun, Brian J. Montz, Ryan Selhorst, Hai-Yan Tang, Jiaxin Zhu, Kelly P. Nevin, Trevor L. Woodard, Alexander E. Ribbe, Thomas P. Russell, Stephen S. Nonnenmann, Derek R. Lovley, Todd Emrick
Summary: Protein-based electronic biomaterials offer environmentally friendly alternatives to traditional metallic and semiconductor materials, but face challenges in processing proteins in organic solvents and forming high-order structures. This study addresses these challenges by forming one-dimensional bundles of electrically conductive protein nanowires harvested from bacteria, enabling the production of multi-scale structures.
Review
Microbiology
Maira Goytia, Crista B. Wadsworth
Summary: The increasing antimicrobial resistance in Neisseria gonorrhoeae poses a direct threat to global public health. Studying nonpathogenic commensal Neisseria can provide insights into resistance mechanisms and help in monitoring and research on pathogenic Neisseria.
Article
Multidisciplinary Sciences
Melissa E. Reardon-Robinson, Minh Tan Nguyen, Belkys C. Sanchez, Jerzy Osipiuk, Christian Ruckert, Chungyu Chang, Bo Chen, Rahul Nagvekar, Andrzej Joachimiak, Andreas Tauch, Asis Das, Hung Ton-That
Summary: In many gram-positive Actinobacteria, MdbA plays a crucial role in bacterial viability by catalyzing oxidative folding of exported proteins. However, in Corynebacterium diphtheriae, the deletion of mdbA only affects cell growth at 37°C, suggesting the existence of alternative oxidoreductase enzymes. Through genetic suppressor mutations, we discovered that elevated expression of tsdA can compensate for the loss of mdbA by mediating oxidative folding of pilin and toxin substrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Johann Mignolet, Marion Mathelie-Guinlet, Albertus Viljoen, Yves F. Dufrene
Summary: Bacterial pili motorization is crucial for cellular function, with the Tad pilus playing a key role in survival, evolution, and virulence. By using a novel platform combining fluorescence-based screening and AFM force-clamp spectroscopy, researchers were able to monitor the nanomechanics and dynamics of Tad pilus retraction under high tension, revealing the pilus' ability to retract at high speeds and its role in mediating bacterial cell landing and surface adhesion. The findings suggest a mechanism where pilus retraction actively triggers cell approach and passive hydrophobic interactions promote strong cell-substrate adhesion, potentially saving ATP-based energy.
NANOSCALE HORIZONS
(2021)
Article
Biology
Wenchao Zhang, Mei Luo, Chunying Feng, Huaqing Liu, Hong Zhang, Rachel R. Bennett, Andrew S. Utada, Zhi Liu, Kun Zhao
Summary: The study reveals the critical role of MSHA pili as a brake and anchor during the landing process of Vibrio cholerae in viscoelastic environments. Loss of MSHA pili leads to a more dramatic increase in mean path length in viscoelastic non-Newtonian fluids compared to viscous Newtonian ones.
Article
Biology
Hani Mohammed Ali
Summary: Antibiotics are drugs used to treat bacterial infections, but antibiotic-resistant bacteria have become a major concern. This study utilized in-silico docking screening to identify a potential natural compound that can overcome antibiotic resistance in bacteria.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Review
Microbiology
Courtney K. Ellison, Gregory B. Whitfield, Yves Brun
Summary: This review discusses recent progress in understanding the function, regulation, and mechanisms of T4P dynamics.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Nanoscience & Nanotechnology
Changshun Hou, Chen Xu, Bo Yi, Xin Huang, Chunyan Cao, Youngjin Lee, Sheng Chen, Xi Yao
Summary: The study introduces a new type of mechano-induced assembly nanocomposite coating with strong adhesion, high durability, and high disinfection efficiency. This coating can effectively kill bacteria in a short period of time, providing great help in preventing the spread of pathogens.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Biochemistry & Molecular Biology
George A. Naclerio, Nader S. Abutaleb, Marwa Alhashimi, Mohamed N. Seleem, Herman O. Sintim
Summary: New N-(1,3,4-oxadiazol-2-yl)benzamides (HSGN-237 and HSGN-238) have been discovered as highly potent compounds against Neisseria gonorrhoeae, as well as clinically important Gram-positive bacteria, with outstanding tolerability to human cell lines.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Spectroscopy
Kai-Ni Wei, Qian-Jun Zhang, Yun-Qian Zhang, Xi Zeng, Xin Xiao, Ying Huang, Kai Chen, Zhu Tao
Summary: Atypical luminescent compounds emit light due to clustering and have important research value and potential applications. This study systematically investigated the luminescent properties and mechanism of cucurbit[n]urils (Q[n]s) and confirmed their clustering emission. The self-induced outer-surface interactions of Q[n]s were found to be the driving force behind the clustering emission, and certain substances could weaken this effect.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Microbiology
Alexandra L. Sacharok, Eric A. Porsch, Taylor A. Yount, Orlaith Keenan, Joseph W. St Geme III
Summary: The study confirms that PilC1 and PilC2 are adhesins in the gram-negative bacterium Kingella kingae, and they have adhesive activity and twitching motility, mainly located in the N-terminal domain of the proteins.
Article
Microbiology
Helga Fernandez-Llamosas, Eduardo Diaz, Manuel Carmona
Summary: Efficient crop production is crucial for feeding the growing global population, with the association of bacteria with plants playing a significant role in plant health and agricultural productivity. Endophytic bacteria are commonly found in plants and often have plant growth promotion properties, although the genetic factors involved in plant colonization by these bacteria are not well understood. This study demonstrates the important role of the second messenger cyclic-di-GMP in plant colonization by the endophytic bacterium Azoarcus sp. CIB, paving the way for potential strategies to modulate the interaction between endophytes and their plant hosts.
Article
Microbiology
Lindsey R. Burcham, Jade R. Bath, Caroline A. Werlang, Laurie M. Lyon, Naoko Liu, Christopher Evans, Katharina Ribbeck, Kelly S. Doran
Summary: MUC5B interacts with GBS and promotes barrier function by inhibiting bacterial attachment and ascension in a murine model. The interaction between GBS and mucins is complex and warrants further investigation.
Article
Food Science & Technology
Apramita Devi, K. A. Anu-Appaiah
Summary: This study found that in the production of Shiraz wines, AAV2 yeast has better synergy with the mixed MLF blend of Lp 1 and Oo 1, resulting in wines that are perceived as more complex in aroma and taste.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Microbiology
Jiayi Sun, J. Cristobal Vera, Jenny Drnevich, Yen Ting Lin, Ruian Ke, Christopher B. Brooke
Article
Physics, Multidisciplinary
Hui-Shun Kuan, Wolfram Poenisch, Frank Juelicher, Vasily Zaburdaev
Summary: Studying the dynamics of dense, active cellular aggregates is important in biology due to their prevalence. The continuum theory presented in the study helps us better understand the formation and merging processes of cellular aggregates, providing a general framework for studying their rheology and nonequilibrium dynamics.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Lennart Hilbert, Yuko Sato, Ksenia Kuznetsova, Tommaso Bianucci, Hiroshi Kimura, Frank Julicher, Alf Honigmann, Vasily Zaburdaev, Nadine L. Vastenhouw
Summary: This study observed the dynamics of euchromatin organization in pluripotent zebrafish cells during transcription initiation, revealing that accumulation of RNA induces the formation of transcriptionally active regions that tend to separate from transcriptionally inactive euchromatin, forming smaller scale microphases.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert
Summary: This research used STED super-resolution imaging and the concept of multiplicative cascades to describe the hierarchical packing of chromatin, which can be fully specified using only four parameters. The study found that this description is particularly effective in characterizing euchromatin organization and proposed that this concept can be applied to images of other chromatin types as well.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Charles Gwellem Anchang, Cong Xu, Maria Gabriella Raimondo, Raja Atreya, Andreas Maier, Georg Schett, Vasily Zaburdaev, Simon Rauber, Andreas Ramming
Summary: The increasing incidence rates of immune-mediated inflammatory diseases (IMIDs) are concerning, as current standard immunotherapies only have a 40-60% response rate. Moreover, these therapies require lifelong usage and cannot achieve true disease cure. The development of various OMICs technologies offers hope for improving IMIDs treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Correction
Multidisciplinary Sciences
Lennart Hilbert, Yuko Sato, Ksenia Kuznetsova, Tommaso Bianucci, Hiroshi Kimura, Frank Juelicher, Alf Honigmann, Vasily Zaburdaev, Nadine L. Vastenhouw
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Jacob Neumann, Yen Ting Lin, Abhishek Mallela, Ely F. Miller, Joshua Colvin, Abell T. Duprat, Ye Chen, William S. Hlavacek, Richard G. Posner
Summary: This article presents the implementation of a practical MCMC method in PyBioNetFit for parameterization of mathematical models in biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution and has been successfully applied to real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty.
Article
Mechanics
Yifeng Tian, Yen Ting Lin, Marian Anghel, Daniel Livescu
Summary: Developing reduced-order models for turbulent flows, which contain dynamics over a wide range of scales, is a challenging problem due to the limited knowledge of Mori-Zwanzig (MZ) operators. In this work, a data-driven learning algorithm based on Koopman's description of dynamical systems and Mori's linear projection operator is applied to fully resolved isotropic turbulence datasets to extract the Mori-Zwanzig operators. The results show that prediction errors in numerical experiments are affected by the choice of observables and can be reduced by including the past history of observables in the memory kernel.
Article
Physics, Multidisciplinary
Wolfram Poenisch, Vasily Zaburdaev
Summary: This study presents a computational model of a micron-sized turbine powered by bacteria, showing that the turbine can rotate persistently by the collective dynamics of multiple pili, and can rotate permanently in the same direction by altering the pili binding to the turbine surface.
FRONTIERS IN PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Mai P. Tran, Rakesh Chatterjee, Yannik Dreher, Julius Fichtler, Kevin Jahnke, Lennart Hilbert, Vasily Zaburdaev, Kerstin Gopfrich
Summary: The construction of an artificial cell requires cell division. Although significant progress has been made in achieving reliable compartment division, mechanisms for segregating DNA-encoded information are still in the early stages. In this study, DNA droplets are formed through liquid-liquid phase separation using DNA Y-motifs. The segregation of DNA droplets is achieved by cleaving the connecting components between two populations of DNA Y-motifs. Enzymatic cleavage and photolabile sites are used to control the segregation process in both bulk solutions and cell-sized water-in-oil droplets and giant unilamellar lipid vesicles (GUVs). The speed of segregation is slower under confinement compared to bulk conditions. The ionic strength of the solution and the nucleobase sequences are utilized to regulate the segregation dynamics. The experimental results are validated by a lattice-based theoretical model that simulates the interactions between DNA Y-motif populations. Overall, the engineered DNA droplets reconstituted in GUVs provide a strategy for DNA segregation within bottom-up assembled synthetic cells.
Article
Infectious Diseases
Abhishek Mallela, Yen Ting Lin, William S. Hlavacek
Summary: According to the study, there was a 4-fold difference in the initial contagiousness of COVID-19 across urban areas in the United States.
Meeting Abstract
Immunology
Jennifer J. Luhr, Nils Alex, Lukas Amon, Martin Kraeter, Marketa Kubankova, Erdinc Sezgin, Christian H. K. Lehmann, Lukas Heger, Gordon F. Heidkamp, Ana Suncana Smith, Vasily Zaburdaev, Rainer A. Boeckmann, Ilya Levental, Michael L. Dustin, Christian Eggeling, Jochen Guck, Diana Dudziak
EUROPEAN JOURNAL OF IMMUNOLOGY
(2021)
Article
Physics, Fluids & Plasmas
Judit Clopes, Jaeoh Shin, Marcus Jahnel, Stephan W. Grill, Vasily Zaburdaev
Summary: Recent research has shown that the EEA1 protein switches from a rigid to a flexible conformation upon binding a signaling protein, allowing it to generate a motor-like force to move vesicles. The binding-induced signal may propagate through the protein chain, leading to conformational changes.
Article
Biochemistry & Molecular Biology
Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Marcel Sobucki, Andrei Yu Kobitski, Gerd Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert
Summary: In eukaryotes, the recruitment and pause release of RNA polymerase II (Pol II) are associated with liquid-phase condensation, where regulatory chromatin regions provide surfaces for condensation at concentrations that are too low for canonical liquid-liquid phase separation. Studies using live and super-resolution microscopy in zebrafish embryos have revealed Pol II clusters with various shapes, shedding light on a new theoretical model.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Immunology
Yen Ting Lin, Jacob Neumann, Ely F. Miller, Richard G. Posner, Abhishek Mallela, Cosmin Safta, Jaideep Ray, Gautam Thakur, Supriya Chinthavali, William S. Hlavacek
Summary: Researchers developed a mathematical model to study the transmission of COVID-19 within regional populations and calibrated the model based on daily reports of confirmed cases to support evidence-based policymaking. Using Bayesian inference, they also investigated uncertainty in parameter estimates and forecasts.
EMERGING INFECTIOUS DISEASES
(2021)