Article
Multidisciplinary Sciences
Manuel Hotz, Nathaniel H. Thayer, David G. Hendrickson, Elizabeth L. Schinski, Jun Xu, Daniel E. Gottschling
Summary: This study discovered a previously unappreciated relationship between the number of copies of the ribosomal RNA gene and the replicative lifespan in budding yeast. The data suggest that regulatory mechanisms involving ribosomal DNA copy number limit lifespan and changes in rDNA copy number might explain the effects of lifespan-enhancing mutations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
David C. Duran, Cesar A. Hernandez, Elizabeth Suesca, Ruben Acevedo, Ivon M. Acosta, Diana A. Forero, Francisco E. Rozo, Juan M. Pedraza
Summary: Researchers have designed and fabricated a device that uses the slipstreaming effect to study the growth and aging of yeast cells under minimal mechanical pressure influence. This device is relatively inexpensive and easy to manufacture, helping to eliminate pressure bias in future studies.
Article
Multidisciplinary Sciences
Giansimone Perrino, Sara Napolitano, Francesca Galdi, Antonella La Regina, Davide Fiore, Teresa Giuliano, Mario di Bernardo, Diego di Bernardo
Summary: The authors have successfully achieved long-term synchronization of a population of genetically modified yeast cells using a cyber-genetic system, providing a new avenue for cell cycle synchronization.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Zhen Zhu, Yingying Wang, Ruobo Peng, Pan Chen, Yangye Geng, Bailiang He, Shuiping Ouyang, Ke Zheng, Yimin Fan, Dejing Pan, Nan Jin, Fabian Rudolf, Andreas Hierlemann
Summary: The MiSCA microfluidic single-cell array allows for immobilizing yeast cells in a precisely controlled microenvironment and conducting comparative culturing under the influence of different media and compounds. This system enables parallel sets of experiments and control experiments, as well as comparative experiments under well-defined laminar-perfusion conditions.
Review
Chemistry, Multidisciplinary
Galina Nemova
Summary: This review discusses the optical refrigeration of rare-earth-doped low-phonon micro- and nanocrystals using anti-Stokes fluorescence. Hybrid optical refrigeration, which suppresses both the translational and internal vibrational thermal energy of the particles, is presented as the latest achievement. Laser cooling of nanoparticles is a promising tool for fundamental quantum-mechanical studies, nonequilibrium thermodynamics, and precision measurements of forces.
APPLIED SCIENCES-BASEL
(2022)
Article
Multidisciplinary Sciences
Jakob Peder Pettersen, Eivind Almaas
Summary: Improvements have been made to a new model for predicting the temperature dependence of an organism's metabolic network, addressing the issue of multimodality and highlighting the model's inadequacy in predicting metabolic flux with current experimental data.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Andy Goldschmidt, James Kunert-Graf, Adrian C. Scott, Zhihao Tan, Aimee M. Dudley, J. Nathan Kutz
Summary: Baker's yeast is a model organism for studying morphology at the scale of multi-cell colonies, with texture score development trajectories used for hierarchical clustering.
Article
Optics
X. Hu, J. Guo, L. M. Zhao, J. Ma, D. Y. Tang
Summary: This study reports the first experimental observation of the coexistence of scalar dark and bright solitons in a fiber laser. The properties of the dark and bright solitons, as well as their bound states, were investigated and confirmed through numerical simulations based on the coupled Ginzburg-Landau equations.
Article
Multidisciplinary Sciences
William M. Shaw, Lucie Studena, Kyler Roy, Piotr Hapeta, Nicholas S. McCarty, Alicia E. Graham, Tom Ellis, Rodrigo Ledesma-Amaro
Summary: CRISPR gene activation and inhibition is a powerful synthetic tool for influencing gene expression, with applications in foundational studies, cellular reprogramming, and metabolic engineering. The authors developed a method for inducible expression of multiple gRNAs, increasing the capacity for CRISPR gene activation and inhibition and enhancing flexibility in target gene manipulation. They also created a highly regulated and user-friendly CRISPR toolkit in yeast, enabling simultaneous activation and repression of 11 genes in central metabolism, resulting in a significant increase in succinic acid production.
NATURE COMMUNICATIONS
(2022)
Article
Optics
N. N. H. E. N. Mahmud, N. A. Awang, N. U. H. H. Zulkefli, F. N. M. Hanafiah
Summary: This study presents a method for optically trapping silica gel microparticles using a stable Q-switched fiber laser pulse. By fabricating gold nanoparticles as saturable absorbers, stable Q-switched fiber laser pulses with a frequency of 25.81 kHz were achieved. The microparticles exhibited different attractive trapping forces based on the viscous drag exerted by the laser field. Experimental results confirmed the validity of the numerical model and demonstrated the potential application of the proposed system for absorption microparticle trapping at 1540 nm wavelength.
OPTICS AND LASERS IN ENGINEERING
(2023)
Article
Biochemical Research Methods
Xingyu Xu, Zhen Zhu, Yingying Wang, Yangye Geng, Feng Xu, Mario A. Marchisio, Zixin Wang, Dejing Pan
Summary: Microfluidic methodologies for replicative lifespan determination of budding yeast cells are highly impacted by the robustness of experimental conditions, especially the design of yeast-trapping structures. In this study, an optimized design, the yeast rotation (YRot) trap, was proposed and validated for stable retention of mother cells and hydrodynamic rotation of buds. The integration of denser YRot traps in microchannels could potentially improve experimental conditions for precise RLS determination in yeast aging studies.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Paraskevi Kritsiligkou, Tzu Keng Shen, Tobias P. Dick
Summary: Genetically encoded fluorescent H2O2 probes have advanced the field of redox biology. A comparison between the HyPer7 and roGFP2-Tsa2 Delta CR probes in yeast as a model system revealed significant differences in the dynamics of intracellular probe reduction, with HyPer7 being rapidly reduced by the thioredoxin system and roGFP2-Tsa2 Delta CR being reduced more slowly by the glutathione system. Future side-by-side measurements with both probes may provide insights into the relative activity of the two major cellular reducing systems.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Yu Qiu, Ke Xu, Amir A. Pahlavan, Ruben Juanes
Summary: This article studies the immiscible fluid-fluid displacement on a precisely controlled structured surface in a microfluidic device, serving as an analogue for rough fractures. It is found that surface roughness affects the wetting transition and film formation, leading to different morphologies of undisplaced fluid. The implications of these observations for geologic and technological applications are discussed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
David Bunk, Julian Moriasy, Felix Thoma, Christopher Jakubke, Christof Osman, David Hoerl
Summary: YeastMate is a user-friendly deep learning-based application that can automatically detect and segment Saccharomyces cerevisiae cells and their mating and budding events in microscopy images. It uses Mask R-CNN with a custom segmentation head for subclassification of mother and daughter cells during lifecycle transitions. YeastMate can be used as a Python library or through a standalone application with a graphical user interface (GUI) and a Fiji plugin.
Article
Biotechnology & Applied Microbiology
Hangrui Liu, Xin Xu, Kai Peng, Yuxin Zhang, Lianmei Jiang, Thomas C. Williams, Ian T. Paulsen, James A. Piper, Ming Li
Summary: Yeast has been engineered for cost-effective organic acid production through metabolic engineering and synthetic biology techniques. The use of monodisperse picolitre droplets as bioreactors allows cultivation of yeast at the single-cell level, providing insights into cell-to-cell variations. This approach has the potential to be applied for engineering yeast to produce value-added bioproducts.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Physics, Multidisciplinary
P. Polimeno, M. A. Iati, C. Degli Esposti Boschi, S. H. Simpson, V Svak, O. Brzobohaty, P. Zemanek, O. M. Marago, R. Saija
Summary: Computational results are presented on the spin-dependent optical force component on zinc oxide nanowires trapped in optical tweezers with circularly polarized light. This non-conservative force is perpendicular to the incident light's propagation direction, and is shape-dependent, connected with the imaginary part of the local Poynting vector and the local spin density.
EUROPEAN PHYSICAL JOURNAL PLUS
(2021)
Article
Engineering, Environmental
Yaprak Ozbakir, Alexandr Jonas, Alper Kiraz, Can Erkey
Summary: Efficient utilization of light in photocatalytic chemical processes requires careful optimization of the photocatalytic reactor layout to maximize the interaction between the incident light, photocatalyst, and reactant molecules. A new type of photocatalytic flow microreactor with an integrated light guide has been developed using a hydrophobic composite aerogel monolith. This concept is scalable and shows great potential for carrying out various photocatalytic reactions in both polar and non-polar solvents.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Nanoscience & Nanotechnology
Alexandr Jonas, Zdenek Pilat, Jan Jezek, Silvie Bernatova, Petr Jedlicka, Mehdi Aas, Alper Kiraz, Pavel Zemanek
Summary: The study investigates transportable optofluidic microlasers tunable by an external electric field, based on fluorophore-doped emulsion droplets of radial nematic liquid crystals manipulated by optical tweezers in microfluidic chips. By controlling the electric and thermal stimulation, the spectral tuning response and relaxation process of the lasing liquid crystal droplets are examined. Strong applied electric fields can induce fully reversible phase transitions in the trapped droplets, allowing for the creation of electrically tunable, optically transported microlasers for integrated microphotonic or sensing systems within microfluidic chips.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Analytical
Katarina Rebrosova, Silvie Bernatova, Martin Siler, Magdalena Uhlirova, Ota Samek, Jan Jezek, Veronika Hola, Filip Ruzicka, Pavel Zemanek
Summary: Urinary tract infections are among the most common infections worldwide. This study demonstrates that Raman spectroscopy can be used as a rapid diagnostic tool to differentiate causative agents and determine antimicrobial susceptibility. It holds great potential for clinical diagnostics in the future.
ANALYTICA CHIMICA ACTA
(2022)
Article
Chemistry, Physical
Ianina L. Violi, Luciana P. Martinez, Mariano Barella, Cecilia Zaza, Lukas Chvatal, Pavel Zemanek, Marina V. Gutierrez, Maria Y. Paredes, Alberto F. Scarpettini, Jorge Olmos-Trigo, Valeria R. Pais, Ivan Diaz Noblega, Emiliano Cortes, Juan Jose Saenz, Andrea V. Bragas, Julian Gargiulo, Fernando D. Stefani
Summary: This article reviews the state of the art of optical printing of single nanoparticles and discusses its strengths, limitations, and future perspectives by focusing on four main challenges: printing accuracy, resolution, selectivity, and nanoparticle photostability.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Optics
Petr Jakl, Martin Siler, Jan Jezek, Angel Cifuentes, Johanna Tragardh, Pavel Zemanek, Tomas Cizmar
Summary: This paper demonstrates that combining a relatively small number of transmission matrices (TMs), measured using different internal references, can completely eliminate blind spots in multimode fiber-based endoscopic imaging, resulting in a significant enhancement of imaging quality.
Article
Chemistry, Analytical
Anton Karalko, Peter Kesa, Frantisek Jelinek, Ludek Sefc, Jan Jezek, Pavel Zemanek, Tomas Grus
Summary: The study aims to develop a method to inject CO2 foam that reduces the risk of brain tissue embolism and heart infarction. Compared to iodine contrast agents, CO2 foam has lower complication risks, and the non-linear contrast imaging method can effectively image micron-sized gas microbubbles in the heart.
Article
Optics
Y. Arita, G. D. Bruce, E. M. Wright, S. H. Simpson, P. Zemanek, K. Dholakia
Summary: We have demonstrated a method of all-optical sympathetic cooling of a laser-trapped microsphere to sub-Kelvin temperatures, achieved through optical binding with a feedback-cooled adjacent particle. Our study opens up possibilities for multi-particle quantum entanglement and sensing in levitated optomechanics.
Article
Chemistry, Analytical
Marketa Benesova, Silvie Bernatova, Filip Mika, Zuzana Pokorna, Jan Jezek, Martin Siler, Ota Samek, Filip Ruzicka, Katarina Rebrosova, Pavel Zemanek, Zdenek Pilat
Summary: Efficient separation and identification of pathogenic bacterial strains is crucial for modern society, with applications in medical diagnostics, drug discovery, biodefense, and food safety. A fast and reliable method for antibody-based immobilization of bacteria onto a gold-plated glass surface, followed by detection using strain-specific antibodies linked to SERS-tags, was developed. The procedure utilizes accessible and affordable materials, and shows potential for rapid identification of bacterial pathogens.
Article
Physics, Applied
M. Siler, V. Svak, A. Jonas, S. H. Simpson, O. Brzobohaty, P. Zemanek
Summary: High-quality nanomechanical oscillators can sensitively probe force, mass, or displacement. A general method of Bayesian inference is introduced to infer the force field and environmental parameters in stochastic inertial systems solely based on the recorded noisy positions. The method provides robust results with trajectories 2 orders of magnitude shorter than those typically required by alternative inference schemes.
PHYSICAL REVIEW APPLIED
(2023)
Proceedings Paper
Optics
Silvie Bernatova, Martin Kizovsky, Maria G. Donato, Antonino Foti, Ota Samek, Jan Jezek, Onofrio M. Marago, Pavel Zemanek, Pietro G. Gucciardi
Summary: Optical nano-printing enables the printing of various nanoparticles into arbitrary configurations, utilizing optical forces to push the particles onto a substrate. It can be used to create a sensitive sensor, called an active aggregate, for detecting low concentrations of dyes or plastic nanoparticles.
22ND POLISH-SLOVAK-CZECH OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS
(2022)
Proceedings Paper
Engineering, Ocean
Silvie Bernatova, Martin Kizovsky, Maria Grazia Donato, Antonino Foti, Pavel Zemanek, Ota Samek, Onofrio M. Marago, Jan Jezek, Pietro G. Gucciardi
Summary: This article reports a new optical method for detecting the presence of nanoplastics by using optical aggregation. By utilizing the optical nanoimprinting of plasmonic metal nanoparticles, the detection sensitivity for nanoparticles and molecules can be enhanced.
2022 IEEE INTERNATIONAL WORKSHOP ON METROLOGY FOR THE SEA LEARNING TO MEASURE SEA HEALTH PARAMETERS (METROSEA)
(2022)