Article
Immunology
Yu-Tze Horng, Novaria Sari Dewi Panjaitan, Hui-Ju Chang, Yu-Hong Wei, Chih-Ching Chien, Hung-Chi Yang, Heng-Yuan Chang, Po-Chi Soo
Summary: In this study, the conservation and role of the KP1_4563 homolog, orfX, in Klebsiella pneumoniae biofilm formation were investigated. The results suggest that orfX can inhibit biofilm formation by reducing capsule polysaccharide (CPS) production.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2022)
Review
Microbiology
Yin Li, Ming Ni
Summary: This article discusses the mechanisms of biofilm formation in Klebsiella pneumoniae and its impact on infection treatment. The biofilm produced by K. pneumoniae can shield bacteria from antibiotics and host immune responses, making eradication of the infection more difficult.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Virology
Min Li, Hui Wang, Long Chen, Genglin Guo, Pei Li, Jiale Ma, Rong Chen, Hong Du, Yuqing Liu, Wei Zhang
Summary: In this study, phage P560 isolated from sewage showed specificity for capsule locus type KL47 K. pneumoniae. The capsule depolymerase P560dep derived from phage P560 was able to degrade the capsule polysaccharides of KL47 type K. pneumoniae and inhibit biofilm formation. Additionally, a single dose of P560dep protected mice from lethal challenge and alleviated pathological changes in the lungs and livers of mice infected with KL47 type K. pneumoniae.
Article
Multidisciplinary Sciences
Rei Nakamoto, Jeric Mun Chung Kwan, Jasmine Fei Li Chin, Hui Ting Ong, Josue Flores-Kim, Caroline Midonet, Michael S. VanNieuwenhze, Xue Li Guan, Lok-To Sham
Summary: Many pathogenic bacteria rely on a layer of capsular polysaccharide (CPS) for virulence, with the bacterial tyrosine kinase (BY-kinase) playing a crucial role in regulating capsule synthesis. The interaction between BY-kinase CpsCD and other proteins influences CPS polymer length and peptidoglycan synthesis in Streptococcus pneumoniae. Autophosphorylation of BY-kinases fine-tunes the activity of CpsC, providing spatiotemporal coordination between CPS and PG synthesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Immunology
Tzu-Lung Lin, Feng-Ling Yang, Chien-Tai Ren, Yi-Jiun Pan, Kuo-Shiang Liao, I-Fan Tu, Yu-Pei Chang, Yang-Yu Cheng, Chung-Yi Wu, Shih-Hsiung Wu, Jin-Town Wang
Summary: In this study, researchers successfully retained the immunogenicity of Klebsiella pneumoniae capsule polysaccharide (CPS) by using CPS depolymerases and developed CPS-conjugated vaccines. The vaccines induced anti-CPS antibodies and increased bactericidal activities in mice, providing protection against K. pneumoniae infections.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Immunology
Maria Eduarda Souza Guerra, Giulia Destro, Brenda Vieira, Alice S. Lima, Lucio Fabio Caldas Ferraz, Anders P. Hakansson, Michelle Darrieux, Thiago Rojas Converso
Summary: The ability to form biofilms is crucial for the virulence of Klebsiella pneumoniae, and biofilms play a significant role in bacterial infections. This review discusses the characteristics of K. pneumoniae biofilms, factors influencing their development, and their contribution to infections. It also explores different model systems used to study biofilm formation in this species. The establishment and maintenance of biofilms in K. pneumoniae are influenced by numerous factors, highlighting the importance of this mechanism for bacterial fitness. Some of these factors could be utilized in future vaccines. However, more in vivo models are needed to evaluate the impact of biofilm development on disease pathogenesis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Monika Oleksy-Wawrzyniak, Adam Junka, Malwina Brozyna, Migdal Pawel, Bartlomiej Kwiek, Maciej Nowak, Beata Maczynska, Marzenna Bartoszewicz
Summary: Urinary infections related to bacterial biofilm on catheters can lead to health problems and economic burden for hospitals. This study evaluated the ability of Klebsiella pneumoniae to form biofilm on various surfaces, including catheters, and tested compounds to remove biofilm. The results showed the importance of intraspecies variability in biofilm formation and susceptibility to antibiotics, and emphasized the role of mechanical flushing and local antimicrobials in removing biofilm.
Article
Microbiology
Jinfeng Bao, Lu Xie, Yating Ma, Ran An, Bing Gu, Chengbin Wang
Summary: This study investigates the changes in cefiderocol resistant Klebsiella pneumoniae using proteomic and transcriptomic analyses. The results show that cefiderocol resistance leads to a decrease in biofilm formation ability, which may be associated with the downregulation of related genes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Infectious Diseases
Ana Gual-de-Torrella, Mercedes Delgado-Valverde, Patricia Perez-Palacios, Jesus Oteo-Iglesias, Estrella Rojo-Molinero, Maria Dolores Macia, Antonio Oliver, Alvaro Pascual, Felipe Fernandez-Cuenca
Summary: This study investigated the role of mrkA adhesin expression, biofilm production, biofilm viability, and biocides in carbapenemase-producing Klebsiella pneumoniae isolates. The results showed that biofilm formation and viability were affected by temperature, with higher rates at 25 degrees Celsius compared to 37 degrees Celsius. Humidity had little effect on biofilm formation. HR clones were more likely to be biofilm producers compared to non-HR clones. Povidone-iodine was found to be effective in reducing biofilm production and thickness.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Article
Immunology
Derek Fleming, Brandon Niese, Whitni Redman, Emily Vanderpool, Vernita Gordon, Kendra P. Rumbaugh
Summary: The absence of the exopolysaccharides Pel and Psl in Pseudomonas aeruginosa did not significantly affect the severity or wound closure rates of wound infections in a mouse model. However, the size and distribution of biofilm aggregates in the wound tissue were different, and the mutants' ability to survive antibiotic treatment was impaired.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Engineering, Geological
Yong-Min Kim, Tae-Hyuk Kwon
Summary: The use of bacterial biofilms and EPS for engineered bioclogging in geotechnical practices has gained attention, with the addition of fine clay particles enhancing the durability of biofilm-induced bioclogging. Experiments showed that biofilm associated with bentonite particles demonstrated improved resistance against fluid flows compared to biofilms alone, suggesting the potential of bentonite-biofilm aggregations in enhancing bioclogging durability in nutrient-poor conditions.
Article
Infectious Diseases
Carolina Sabenca, Eliana Costa, Sara Sousa, Lillian Barros, Ana Oliveira, Sonia Ramos, Gilberto Igrejas, Carmen Torres, Patricia Poeta
Summary: The emergence of Klebsiella pneumoniae strains producing ESBL and KPC has become a major public health concern. The ability of these strains to form biofilms is worrisome as it can facilitate the spread of antibiotic resistance and prolong infections in healthcare facilities.
Article
Biology
Amandine Buffet, Eduardo P. C. Rocha, Olaya Rendueles
Summary: The research highlights that capsule inactivation is more frequent in nutrient-rich environments, but provides a clear fitness advantage in nutrient-poor conditions by increasing growth rates and population yields. The study also reveals complex interactions between the environment, genetic background, and serotype in relation to bacterial capsules.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Infectious Diseases
Teresa Fasciana, Andrea Ciammaruconi, Bernardina Gentile, Paola Di Carlo, Roberta Virruso, Maria Rita Tricoli, Daniela Maria Palma, Giovanna Laura Pitarresi, Florigio Lista, Anna Giammanco
Summary: The rapid identification and characterization of multidrug-resistant Klebsiella pneumoniae strains is crucial for diagnosing severe infections in patients. Traditional methods such as pulsed-field gel electrophoresis or multilocus sequence typing are time-consuming, laborious, and expensive, while next-generation sequencing has emerged as a faster and more cost-effective alternative.
Article
Immunology
Zhijie Zhang, Hairui Wang, Yawen Guo, Zhaoyu Liu, Zhihui Chang
Summary: This study found significant differences in bacterial characteristics between IKPLA and KPLA, including microbiological changes, activation of related metabolic pathways, and expression of pathogenic genes. These differences provide clues for exploring the mechanism of invasiveness in KPLA.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Mechanics
Keara T. Saud, Mahesh Ganesan, Michael J. Solomon
Summary: The study examines the yield stress behavior of colloidal gels with embedded active particles, finding that the presence of active particles leads to significant softening of the gel, especially at low ratios of active to passive particles.
JOURNAL OF RHEOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Daniel A. Messenger, David M. Bortz
Summary: Sparse Identification of Nonlinear Dynamics (SINDy) has been extended to the weak formulation for partial differential equations (PDEs) to improve accuracy in model coefficient recovery and robustness in identifying PDEs in large noise regime. The implementation utilizes Fast Fourier Transform for efficient model identification and reveals a connection between noise robustness and spectra of test functions. Additionally, a learning algorithm for threshold in sequential thresholding least-squares (STLS) is introduced for model identification from large libraries.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Chemistry, Physical
Tianyu Liu, Tianyu Liu, Fengyi Gao, Sharon C. Glotzer, Michael J. Solomon
Summary: Introducing discoidal shape anisotropy into colloidal particles can alter structural color reflection, with the shape and size of discoids affecting the orderliness of assembled structures and color effects.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Tianyu Liu, Bryan VanSaders, Jacob T. Keating, Sharon C. Glotzer, Michael J. Solomon
Summary: This study investigates the impact of irregularly sized particles on the microstructural quality and structural color reflectivity of colloidal crystals formed by evaporative self-assembly. It is found that small irregular particles have a more detrimental effect on surface crystal quality and structural color reflectivity compared to large irregular particles. The study also shows that the overall crystallinity of assembled structures increases with the peak reflectivity and is correlated with the volume fraction of irregular particles.
Article
Chemistry, Physical
Peng-Kai Kao, Michael J. Solomon, Mahesh Ganesan
Summary: The study demonstrates that changing the shape of building blocks from spheres to discoids can significantly increase the elastic modulus of colloidal gels. Through modeling fractal cluster gel rheology, it is revealed that the impact of shape anisotropy on gel elasticity is due to the combined effects on the microstructure of the gel network, the anisotropy of attractive interparticle pair potentials, and the volumetric compactness of the fractal cluster.
Article
Multidisciplinary Sciences
Graycen E. Wheeler, Amrita Purkayastha, Eric N. Bunker, David M. Bortz, Xuedong Liu
Summary: This study describes a method for measuring and quantifying single-cell and bulk motility of HaCaT keratinocytes using a nuclear stain. The method includes a MATLAB script for analyzing TrackMate output files to calculate displacements, motility rates, and trajectory angles, allowing for quick, straightforward, and scalable analysis of cell motility rates.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Mechanics
Joanne K. Beckwith, Mahesh Ganesan, J. Scott VanEpps, Anuj Kumar, Michael J. Solomon
Summary: This study presents a method to measure the mechanical properties of Candida albicans biofilms and demonstrates its performance. The method allows researchers to investigate the effects of genetic, phenotypic, and environmental factors on the material properties of fungal biofilms, which is crucial for understanding their growth and developing remediation strategies.
JOURNAL OF RHEOLOGY
(2022)
Article
Mathematics, Applied
Jacqueline Wentz, Jeffrey C. Cameron, David M. Bortz
Summary: This research presents an analytical singular value decomposition method for the stoichiometry matrix of a reaction-diffusion system to reveal spatial flux patterns. Approaches for approximate and exact singular value decompositions are studied for different reaction and diffusion scenarios. The study shows that the singular value decomposition depends on smaller matrix decompositions, providing efficient analysis of the stoichiometry matrix of reaction-diffusion systems.
SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS
(2022)
Article
Mathematics, Applied
Daniel A. Messenger, David M. Bortz
Summary: We have developed a weak-form sparse identification method for interacting particle systems (IPS), aiming to reduce computational complexity for large number of particles and offer robustness to noise. By combining mean-field theory of IPS with the weak-form sparse identification of nonlinear dynamics algorithm (WSINDy), we provide a fast and reliable system identification scheme for recovering the governing stochastic differential equations for an IPS.
PHYSICA D-NONLINEAR PHENOMENA
(2022)
Article
Chemistry, Multidisciplinary
Tianyu Liu, Michael J. Solomon
Summary: Self-assembled colloidal crystals exhibit structural colors due to light diffraction from their ordered microscale structure. This study identifies the design space for creating grating diffraction (GD) structural colors and demonstrates their relative advantages. Using electrophoretic deposition, crystals with fine grains are self-assembled from 1.0 μm diameter colloids. The transmitted structural color is tunable across the visible spectrum, with the best optical response observed at low layer numbers (<= 5 layers). The spectral response can be well predicted by Mie scattering of the crystals. The results highlight the potential of micron-sized colloids to produce vivid grating colors with high saturation, expanding the possibilities of artificial structural color materials.
Article
Chemistry, Applied
Keara T. Saud, Jin Xu, Sabina Wilkanowicz, Yue He, James J. Moon, Michael J. Solomon
Summary: Recent studies have shown that inulin has a prebiotic effect by selectively promoting bacteria in the colon, modulating the gut microbiome, and generating beneficial effects on gastrointestinal inflammation, diabetes, and cancer. However, the water-soluble nature of inulin limits its prebiotic effect due to low delivery efficiency and short retention time in the colon. This study aimed to produce inulin microparticles (MPs) using the electrospray method and evaluate their material properties and bioavailability.
FOOD HYDROCOLLOIDS
(2023)
Article
Multidisciplinary Sciences
Daniel A. Messenger, Graycen E. Wheeler, Xuedong Liu, David M. Bortz
Summary: Researchers have developed the WSINDy method to learn equations for communities of cells and classify them using a novel scheme. The method demonstrates efficiency and proficiency through various test scenarios.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Mathematics, Interdisciplinary Applications
Daniel A. Messenger, David M. Bortz
Summary: A novel weak formulation and discretization method, called WSINDy, is proposed to discover governing equations from noisy measurement data. Compared to the standard SINDy algorithm, WSINDy allows for reliable model identification and reduces errors in data with large noise levels.
MULTISCALE MODELING & SIMULATION
(2021)
Article
Immunology
Andrea G. Buchwald, Jude Bayham, Jimi Adams, David Bortz, Kathryn Colborn, Olivia Zarella, Meghan Buran, Jonathan Samet, Debashis Ghosh, Rachel Herlihy, Elizabeth J. Carlton
Summary: The study conducted in Colorado showed that early policy measures related to COVID-19 significantly decreased mobility and reduced virus transmission, with the effective reproductive number falling below 1. Although mobility increased to near baseline levels after some restrictions were lifted, transmission remained low. As the model parameters were adjusted to better reflect the reality in Colorado over time, there were modest changes in estimates of intervention effects and more conservative long-term projections.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Mathematics, Applied
Jacqueline M. Wentz, David M. Bortz
Summary: This study focuses on determining sufficient conditions to guarantee that the discrete reaction-diffusion system is bounded for all time, using a Lyapunov-like function on a 1D domain with homogeneous Neumann boundary conditions and nonnegative initial data and solutions. The existence of this function ensures the boundedness of the system, as illustrated in the context of four example systems.
SIAM JOURNAL ON APPLIED MATHEMATICS
(2021)