Tutorial for the growth and development of Myxococcus xanthus as a Model System at the Intersection of Biology and Physics
Jesus Manuel Antúnez Domínguez, Laura Pérez García, Natsuko Rivera-Yoshida, Jasmin Di Franco, David Steiner, Alejandro V. Arzola, Mariana Benítez, Charlotte Hamngren Blomqvist, Roberto Cerbino, Caroline Beck Adiels, Giovanni Volpe
arXiv: 2407.18714
Myxococcus xanthus is a unicellular organism whose cells possess the ability to move and communicate, leading to the emergence of complex collective properties and behaviours. This has made it an ideal model system to study the emergence of collective behaviours in interdisciplinary research efforts lying at the intersection of biology and physics, especially in the growing field of active matter research. Often, challenges arise when setting up reliable and reproducible culturing protocols. This tutorial provides a clear and comprehensive guide on the culture, growth, development, and experimental sample preparation of M. xanthus. Additionally, it includes some representative examples of experiments that can be conducted using these samples, namely motility assays, fruiting body formation, predation, and elasticotaxis.
Optimal calibration of optical tweezers with arbitrary integration time and sampling frequencies — A general framework
Laura Pérez-García, Martin Selin, Antonio Ciarlo, Alessandro Magazzù, Giuseppe Pesce, Antonio Sasso, Giovanni Volpe, Isaac Pérez Castillo, Alejandro V. Arzola
Biomedical Optics Express, 14, 6442-6469 (2023)
doi: 10.1364/BOE.495468
arXiv: 2305.07245
Optical tweezers (OT) have become an essential technique in several fields of physics, chemistry, and biology as precise micromanipulation tools and microscopic force transducers. Quantitative measurements require the accurate calibration of the trap stiffness of the optical trap and the diffusion constant of the optically trapped particle. This is typically done by statistical estimators constructed from the position signal of the particle, which is recorded by a digital camera or a quadrant photodiode. The finite integration time and sampling frequency of the detector need to be properly taken into account. Here, we present a general approach based on the joint probability density function of the sampled trajectory that corrects exactly the biases due to the detector’s finite integration time and limited sampling frequency, providing theoretical formulas for the most widely employed calibration methods: equipartition, mean squared displacement, autocorrelation, power spectral density, and force reconstruction via maximum-likelihood-estimator analysis (FORMA). Our results, tested with experiments and Monte Carlo simulations, will permit users of OT to confidently estimate the trap stiffness and diffusion constant, extending their use to a broader set of experimental conditions.
Roadmap for optical tweezers
Giovanni Volpe, Onofrio M Maragò, Halina Rubinsztein-Dunlop, Giuseppe Pesce, Alexander B Stilgoe, Giorgio Volpe, Georgiy Tkachenko, Viet Giang Truong, Síle Nic Chormaic, Fatemeh Kalantarifard, Parviz Elahi, Mikael Käll, Agnese Callegari, Manuel I Marqués, Antonio A R Neves, Wendel L Moreira, Adriana Fontes, Carlos L Cesar, Rosalba Saija, Abir Saidi, Paul Beck, Jörg S Eismann, Peter Banzer, Thales F D Fernandes, Francesco Pedaci, Warwick P Bowen, Rahul Vaippully, Muruga Lokesh, Basudev Roy, Gregor Thalhammer-Thurner, Monika Ritsch-Marte, Laura Pérez García, Alejandro V Arzola, Isaac Pérez Castillo, Aykut Argun, Till M Muenker, Bart E Vos, Timo Betz, Ilaria Cristiani, Paolo Minzioni, Peter J Reece, Fan Wang, David McGloin, Justus C Ndukaife, Romain Quidant, Reece P Roberts, Cyril Laplane, Thomas Volz, Reuven Gordon, Dag Hanstorp, Javier Tello Marmolejo, Graham D Bruce, Kishan Dholakia, Tongcang Li, Oto Brzobohatý, Stephen H Simpson, Pavel Zemánek, Felix Ritort, Yael Roichman, Valeriia Bobkova, Raphael Wittkowski, Cornelia Denz, G V Pavan Kumar, Antonino Foti, Maria Grazia Donato, Pietro G Gucciardi, Lucia Gardini, Giulio Bianchi, Anatolii V Kashchuk, Marco Capitanio, Lynn Paterson, Philip H Jones, Kirstine Berg-Sørensen, Younes F Barooji, Lene B Oddershede, Pegah Pouladian, Daryl Preece, Caroline Beck Adiels, Anna Chiara De Luca, Alessandro Magazzù, David Bronte Ciriza, Maria Antonia Iatì, Grover A Swartzlander Jr
Journal of Physics: Photonics 2(2), 022501 (2023)
arXiv: 2206.13789
doi: 110.1088/2515-7647/acb57b
Optical tweezers are tools made of light that enable contactless pushing, trapping, and manipulation of objects, ranging from atoms to space light sails. Since the pioneering work by Arthur Ashkin in the 1970s, optical tweezers have evolved into sophisticated instruments and have been employed in a broad range of applications in the life sciences, physics, and engineering. These include accurate force and torque measurement at the femtonewton level, microrheology of complex fluids, single micro- and nano-particle spectroscopy, single-cell analysis, and statistical-physics experiments. This roadmap provides insights into current investigations involving optical forces and optical tweezers from their theoretical foundations to designs and setups. It also offers perspectives for applications to a wide range of research fields, from biophysics to space exploration.
The environment topography alters the transition from single-cell populations to multicellular structures in Myxococcus xanthus
Karla C. Hernández Ramos, Edna Rodríguez-Sánchez, Juan Antonio Arias del Angel, Alejandro V. Arzola, Mariana Benítez, Ana E. Escalante, Alessio Franci, Giovanni Volpe, Natsuko Rivera-Yoshida
Sci. Adv. 7(35), eabh2278 (2021)
bioRxiv: 10.1101/2021.01.27.428527
doi: 10.1126/sciadv.abh2278
The social soil-dwelling bacteria Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physico-chemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus. In topographies realized by randomly placing silica particles over agar plates, we observe that the cells’ interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size and shape of the fruiting bodies, and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a minimal computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological and medical relevance.
Optical Tweezers: A Comprehensive Tutorial from Calibration to Applications
Jan Gieseler, Juan Ruben Gomez-Solano, Alessandro Magazzù, Isaac Pérez Castillo, Laura Pérez García, Marta Gironella-Torrent, Xavier Viader-Godoy, Felix Ritort, Giuseppe Pesce, Alejandro V. Arzola, Karen Volke-Sepulveda & Giovanni Volpe
Advances in Optics and Photonics, 13(1), 74-241 (2021)
doi: https://doi.org/10.1364/AOP.394888
arXiv: 2004.05246
Since their invention in 1986 by Arthur Ashkin and colleagues, optical tweezers have become an essential tool in several fields of physics, spectroscopy, biology, nanotechnology, and thermodynamics. In this Tutorial, we provide a primer on how to calibrate optical tweezers and how to use them for advanced applications. After a brief general introduction on optical tweezers, we focus on describing and comparing the various available calibration techniques. Then, we discuss some cutting-edge applications of optical tweezers in a liquid medium, namely to study single-molecule and single-cell mechanics, microrheology, colloidal interactions, statistical physics, and transport phenomena. Finally, we consider optical tweezers in vacuum, where the absence of a viscous medium offers vastly different dynamics and presents new challenges. We conclude with some perspectives for the field and the future application of optical tweezers. This Tutorial provides both a step-by-step guide ideal for non-specialists entering the field and a comprehensive manual of advanced techniques useful for expert practitioners. All the examples are complemented by the sample data and software necessary to reproduce them.
Aykut Argun
Calibration of force fields using recurrent neural networks
26 August 2020, 8:30 AM
SPIE Link: here.
Laura Pérez-García
Deep-learning enhanced light-sheet microscopy
25 August 2020, 9:10 AM
SPIE Link: here.
Daniel Midtvedt
Holographic characterization of subwavelength particles enhanced by deep learning
24 August 2020, 2:40 PM
SPIE Link: here.
Benjamin Midtvedt
DeepTrack: A comprehensive deep learning framework for digital microscopy
26 August 2020, 11:40 AM
SPIE Link: here.
Gorka Muñoz-Gil
The anomalous diffusion challenge: Single trajectory characterisation as a competition
26 August 2020, 12:00 PM
SPIE Link: here.
Meera Srikrishna
Brain tissue segmentation using U-Nets in cranial CT scans
25 August 2020, 2:00 PM
SPIE Link: here.
Juan S. Sierra
Automated corneal endothelium image segmentation in the presence of cornea guttata via convolutional neural networks
26 August 2020, 11:50 AM
SPIE Link: here.
Harshith Bachimanchi
Digital holographic microscopy driven by deep learning: A study on marine planktons (Poster)
24 August 2020, 5:30 PM
SPIE Link: here.
Laura Pérez-García
Reconstructing complex force fields with optical tweezers
24 August 2020, 5:00 PM
SPIE Link: here.
Alejandro V. Arzola
Direct visualization of the spin-orbit angular momentum conversion in optical trapping
25 August 2020, 10:40 AM
SPIE Link: here.
Isaac Lenton
Illuminating the complex behaviour of particles in optical traps with machine learning
26 August 2020, 9:10 AM
SPIE Link: here.
Fatemeh Kalantarifard
Optical trapping of microparticles and yeast cells at ultra-low intensity by intracavity nonlinear feedback forces
24 August 2020, 11:10 AM
SPIE Link: here.
Note: the presentation times are indicated according to PDT (Pacific Daylight Time) (GMT-7)
High-Performance Reconstruction of Microscopic Force Fields from Brownian Trajectories Laura Pérez García, Jaime Donlucas Pérez, Giorgio Volpe, Alejandro V. Arzola & Giovanni Volpe
Nature Communications 9, 5166 (2018)
doi: 10.1038/s41467-018-07437-x
arXiv: 1808.05468
The accurate measurement of microscopic force fields is crucial in many branches of science and technology, from biophotonics and mechanobiology to microscopy and optomechanics. These forces are often probed by analysing their influence on the motion of Brownian particles. Here we introduce a powerful algorithm for microscopic force reconstruction via maximum-likelihood-estimator analysis (FORMA) to retrieve the force field acting on a Brownian particle from the analysis of its displacements. FORMA estimates accurately the conservative and non-conservative components of the force field with important advantages over established techniques, being parameter-free, requiring ten-fold less data and executing orders-of-magnitude faster. We demonstrate FORMA performance using optical tweezers, showing how, outperforming other available techniques, it can identify and characterise stable and unstable equilibrium points in generic force fields. Thanks to its high performance, FORMA can accelerate the development of microscopic and nanoscopic force transducers for physics, biology and engineering.
Alejandro V. Arzola is a Visiting Professor from the Universidad Nacional Autónoma de México in Mexico City. His visiting position is financed through the Linnaeus Palme International Exchange Programme.
Alejandro was born in Oaxaca in the south of Mexico. He studied for a PhD at the Universidad Nacional Autónoma de México (UNAM) in Mexico City, worked as a posdoctoral researcher at the Institutte of Scientific Instruments in Brno, Czech Republic, and at UNAM. Since 2014 he joined the group of Optical Micromanipulation at the Institute of Physics in UNAM.
He is interested in optical micromanipulation and related research fields. His latest research deals with the transport of Brownian particles in optical landscapes under breaking space-time symmetries, a system which is known in the literature as ratchets. He is also interested in the behavior of microscopic particles in structured light fields with spin and orbital angular momentum.