High-contrast Brillouin and Raman micro-spectroscopy for simultaneous mechanical and chemical investigation of microbial biofilms

Uncertainty Estimation for the Brillouin Frequency Shift Measurement Using a Scanning Tandem Fabry-Pérot Interferometer

The expanded uncertainty of the measured Brillouin scattering shift frequencies is essential in assessing the measurements of parameters of various materials. We describe the general operation principles of a Brillouin light scattering (BLS) spectrometer with a high-power laser and a scanning tandem Fabry-Pérot interferometer (TFPI) for material characterization. Various uncertainty components have been analyzed for the BLS spectrometer following the Guide to the Expression of Uncertainty in Measurement (GUM). The expanded relative uncertainty in the measured Brillouin frequency shift of 15.70 GHz for polymethyl methacrylate (PMMA) was estimated to be 0.26%. The calculated Brillouin frequency shift (based on material properties of PMMA) was determined to be 15.44 GHz with expanded relative uncertainty of 2.13%. It was shown that the measured and calculated Brillouin frequency shifts for PMMA agree within their expanded uncertainties. The TFPI-based BLS spectrometer can be used to measure the longitudinal modulus of materials with an expanded uncertainty of 1.9%, which is smaller than that of the ultrasonic velocity-based method (estimated to be 2.9%).

Yeast biofilms on abiotic surfaces: Adhesion factors and control methods

Biofilms are highly resistant to antimicrobials and are a common problem in many industries, including pharmaceutical, food and beverage. Yeast biofilms can be formed by various yeast species, including Candida albicans, Saccharomyces cerevisiae, and Cryptococcus neoformans. Yeast biofilm formation is a complex process that involves several stages, including reversible adhesion, followed by irreversible adhesion, colonization, exopolysaccharide matrix formation, maturation and dispersion. Intercellular communication in yeast biofilms (quorum-sensing mechanism), environmental factors (pH, temperature, composition of the culture medium), and physicochemical factors (hydrophobicity, Lifshitz-van der Waals and Lewis acid-base properties, and electrostatic interactions) are essential to the adhesion process. Studies on the adhesion of yeast to abiotic surfaces such as stainless steel, wood, plastic polymers, and glass are still scarce, representing a gap in the field. The biofilm control formation can be a challenging task for food industry. However, some strategies can help to reduce biofilm formation, such as good hygiene practices, including regular cleaning and disinfection of surfaces. The use of antimicrobials and alternative methods to remove the yeast biofilms may also be helpful to ensure food safety. Furthermore, physical control measures such as biosensors and advanced identification techniques are promising for yeast biofilms control. However, there is a gap in understanding why some yeast strains are more tolerant or resistant to sanitization methods. A better understanding of tolerance and resistance mechanisms can help researchers and industry professionals to develop more effective and targeted sanitization strategies to prevent bacterial contamination and ensure product quality. This review aimed to identify the most important information about yeast biofilms in the food industry, followed by the removal of these biofilms by antimicrobial agents. In addition, the review summarizes the alternative sanitizing methods and future perspectives for controlling yeast biofilm formation by biosensors.

Brillouin-Raman micro-spectroscopy and machine learning techniques to classify osteoarthritic lesions in the human articular cartilage

In this study, Brillouin and Raman micro-Spectroscopy (BRamS) and Machine Learning were used to set-up a new diagnostic tool for Osteoarthritis (OA), potentially extendible to other musculoskeletal diseases. OA is a degenerative pathology, causing the onset of chronic pain due to cartilage disruption. Despite this, it is often diagnosed late and the radiological assessment during the routine examination may fail to recognize the threshold beyond which pharmacological treatment is no longer sufficient and prosthetic replacement is required. Here, femoral head resections of OA-affected patients were analyzed by BRamS, looking for distinctive mechanical and chemical markers of the progressive degeneration degree, and the result was compared to standard assignment via histological staining. The procedure was optimized for diagnostic prediction by using a machine learning algorithm and reducing the time required for measurements, paving the way for possible future in vivo characterization of the articular surface through endoscopic probes during arthroscopy.

Microscale mechanochemical characterization of drying oil films by in situ correlative Brillouin and Raman spectroscopy

Correlative Brillouin and Raman microspectroscopy (BRaMS) is applied for the in situ monitoring of the chemical and physical changes of linseed oil during polymerization. The viscoelastic properties of the drying oil throughout the phase transition were determined by Brillouin light scattering (BLS) and joined to the Raman spectroscopic information about the chemical process responsible for the oil hardening. A comparative study was then performed on an oil mock-up containing ZnO, one of the most common white pigments used in cultural heritage. The intriguing outcomes open new research perspectives for a deeper comprehension of the processes leading to the conversion of a fluid binder into a dry adhering film. The description of both chemical and structural properties of the polymeric network and their evolution are the basis for a better understanding of oil painting degradation. Last, as a feasibility test, BRaMS was applied to study a precious microfragment from J. Pollock's masterpiece Alchemy.

Detection and Characterization of Bacterial Biofilms and Biofilm-Based Sensors

Microbial biofilms have caused serious concerns in healthcare, medical, and food industries because of their intrinsic resistance against conventional antibiotics and cleaning procedures and their capability to firmly adhere on surfaces for persistent contamination. These global issues strongly motivate researchers to develop novel methodologies to investigate the kinetics underlying biofilm formation, to understand the response of the biofilm with different chemical and physical treatments, and to identify biofilm-specific drugs with high-throughput screenings. Meanwhile microbial biofilms can also be utilized positively as sensing elements in cell-based sensors due to their strong adhesion on surfaces. In this perspective, we provide an overview on the connections between sensing and microbial biofilms, focusing on tools used to investigate biofilm properties, kinetics, and their response to chemicals or physical agents, and biofilm-based sensors, a type of biosensor using the bacterial biofilm as a biorecognition element to capture the presence of the target of interest by measuring the metabolic activity of the immobilized microbial cells. Finally we discuss possible new research directions for the development of robust and rapid biofilm related sensors with high temporal and spatial resolutions, pertinent to a wide range of applications.

Brillouin-Raman microspectroscopy for the morpho-mechanical imaging of human lamellar bone

Bone has a sophisticated architecture characterized by a hierarchical organization, starting at the sub-micrometre level. Thus, the analysis of the mechanical and structural properties of bone at this scale is essential to understand the relationship between its physiology, physical properties and chemical composition. Here, we unveil the potential of Brillouin-Raman microspectroscopy (BRaMS), an emerging correlative optical approach that can simultaneously assess bone mechanics and chemistry with micrometric resolution. Correlative hyperspectral imaging, performed on a human diaphyseal ring, reveals a complex microarchitecture that is reflected in extremely rich and informative spectra. An innovative method for mechanical properties analysis is proposed, mapping the intermixing of soft and hard tissue areas and revealing the coexistence of regions involved in remodelling processes, nutrient transportation and structural support. The mineralized regions appear elastically inhomogeneous, resembling the pattern of the osteons' lamellae, while Raman and energy-dispersive X-ray images through scanning electron microscopy show an overall uniform distribution of the mineral content, suggesting that other structural factors are responsible for lamellar micromechanical heterogeneity. These results, besides giving an important insight into cortical bone tissue properties, highlight the potential of BRaMS to access the origin of anisotropic mechanical properties, which are almost ubiquitous in other biological tissues.

Brillouin and Raman Micro-Spectroscopy: A Tool for Micro-Mechanical and Structural Characterization of Cortical and Trabecular Bone Tissues

Human bone is a specialized tissue with unique material properties, providing mechanical support and resistance to the skeleton and simultaneously assuring capability of adaptation and remodelling. Knowing the properties of such a structure down to the micro-scale is of utmost importance, not only for the design of effective biomimetic materials but also to be able to detect pathological alterations in material properties, such as micro-fractures or abnormal tissue remodelling. The Brillouin and Raman micro-spectroscopic (BRmS) approach has the potential to become a first-choice technique, as it is capable of simultaneously investigating samples’ mechanical and structural properties in a non-destructive and label-free way. Here, we perform a mapping of cortical and trabecular bone sections of a femoral epiphysis, demonstrating the capability of the technique for discovering the morpho-mechanics of cells, the extracellular matrix, and marrow constituents. Moreover, the interpretation of Brillouin and Raman spectra merged with an approach of data mining is used to compare the mechanical alterations in specimens excised from distinct anatomical areas and subjected to different sample processing. The results disclose in both cases specific alterations in the morphology and/or in the tissue chemical make-up, which strongly affects bone mechanical properties, providing a method potentially extendable to other important biomedical issues.

How does temperature trigger biofilm adhesion and growth in Candida albicans and two non-Candida albicans Candida species?

BACKGROUND

Biofilm formation on biotic and abiotic surfaces is finely regulated by genetic factors but also by oxygen concentration, pH, temperature and other environmental factors, already extensively explored for bacterial biofilms. Much less is known about fungal biofilm, that is considered a virulence factor for Candida pathogenic species among the few fungal species able to grow and survive at high temperatures such as 37°C as well as those induced by fever. The resistance to high temperatures coupled with the ability to form biofilm are threatening factors of these fungal species that could severely impact at an epidemiological level.

OBJECTIVES

In this framework, we decided to study the thermal tolerance of biofilms formed by three medical relevant species such as Candida albicans and two non-Candida albicans Candida species.

METHODS

Thirty nosocomial strains were investigated for their ability to adhere and grow in proximity and over body temperature (from 31 to 43°C), mimicking different environmental conditions or severe febrile-like reactions.

RESULTS

Candida sessile cells reacted to different temperatures showing a strain-specific response. It was observed that the attachment and growth respond differently to the temperature and that mechanism of adhesion has different outputs at high temperature than the growth.

CONCLUSIONS

This strain-dependent response is probably instrumental to guarantee the best success to cells for the infection, attachment and growth to occur. These observations reinforce the concept of temperature as a major trigger in the evolution of these species especially in this period of increasing environmental temperatures and excessive domestic heating.

Brillouin Spectroscopy: From Biomedical Research to New Generation Pathology Diagnosis

Brillouin spectroscopy has recently gained considerable interest within the biomedical field as an innovative tool to study mechanical properties in biology. The Brillouin effect is based on the inelastic scattering of photons caused by their interaction with thermodynamically driven acoustic modes or phonons and it is highly dependent on the material's elasticity. Therefore, Brillouin is a contactless, label-free optic approach to elastic and viscoelastic analysis that has enabled unprecedented analysis of ex vivo and in vivo mechanical behavior of several tissues with a micrometric resolution, paving the way to a promising future in clinical diagnosis. Here, we comprehensively review the different studies of this fast-moving field that have been performed up to date to provide a quick guide of the current literature. In addition, we offer a general view of Brillouin's biomedical potential to encourage its further development to reach its implementation as a feasible, cost-effective pathology diagnostic tool.

Microsystems for biofilm characterization and sensing - A review

Biofilms are the primary cause of clinical bacterial infections and are impervious to typical amounts of antibiotics, necessitating very high doses for elimination. Therefore, it is imperative to have suitable methods for characterization to develop novel methods of treatment that can complement or replace existing approaches using significantly lower doses of antibiotics. This review presents some of the current developments in microsystems for characterization and sensing of bacterial biofilms. Initially, we review current standards for studying biofilms that are based on invasive and destructive end-point biofilm characterization. Additionally, biofilm formation and growth is extremely sensitive to various growth and environmental parameters that cause large variability in biofilms between repeated experiments, making it very difficult to compare experimental repeats and characterize the temporal characteristics of these organisms. To address these challenges, recent developments in the field have moved toward systems and miniature devices that can aid in the non-invasive characterization of bacterial biofilms. Our review focuses on several types of microsystems for biofilm evaluation including optical, electrochemical, and mechanical systems. This review will show how these devices can lead to better understanding of the physiology and function of these communities of bacteria, which can eventually lead to the development of novel treatments that do not rely on high-dosage antibiotics.

Nonlinear rheological characteristics of single species bacterial biofilms

Bacterial biofilms in natural and artificial environments perform a wide array of beneficial or detrimental functions and exhibit resistance to physical as well as chemical perturbations. In dynamic environments, where periodic or aperiodic flows over surfaces are involved, biofilms can be subjected to large shear forces. The ability to withstand these forces, which is often attributed to the resilience of the extracellular matrix. This attribute of the extracellular matrix is referred to as viscoelasticity and is a result of self-assembly and cross-linking of multiple polymeric components that are secreted by the microbes. We aim to understand the viscoelastic characteristic of biofilms subjected to large shear forces by performing Large Amplitude Oscillatory Shear (LAOS) experiments on four species of bacterial biofilms: Bacillus subtilis, Comamonas denitrificans, Pseudomonas fluorescens and Pseudomonas aeruginosa. We find that nonlinear viscoelastic measures such as intracycle strain stiffening and intracycle shear thickening for each of the tested species, exhibit subtle or distinct differences in the plot of strain amplitude versus frequency (Pipkin diagram). The biofilms also exhibit variability in the onset of nonlinear behaviour and energy dissipation characteristics, which could be a result of heterogeneity of the extracellular matrix constituents of the different biofilms. The results provide insight into the nonlinear rheological behaviour of biofilms as they are subjected to large strains or strain rates; a situation that is commonly encountered in nature, but rarely investigated.

Brillouin spectroscopy of biorelevant fluids in relation to viscosity and solute concentration

The measurement of intracellular viscoelastic properties by Brillouin scattering is a rapidly developing field in biophysics and medicine. Here, the Brillouin spectroscopy is applied for a number of aqueous solutions of biorelevant molecules to reveal relations between the Brillouin line parameters (frequency and width) and viscosity or solute concentration. It is found that for the majority of the studied biorelevant molecules the solute concentration governs the Brillouin frequency in a universal manner. On the other hand, the relations between the macroscopic viscosity and Brillouin peak parameters are different for different solutes. We conclude that for biological fluids the viscosity evaluation from Brillouin data needs prior knowledge about the chemical composition. This result challenges the fidelity of the indirect experimental determinations of the cellular viscosity, when small molecule solutions are used for the calibration.

Quantitative imaging and spectroscopic technologies for microbiology

Light microscopy has enabled the observation of the structure and organisation of biofilms. Typically, the contrast in an image obtained from light microscopy is given by the time-averaged intensity that is effective in visualising the overall structure. Technological advancements in light microscopy have led to the creation of techniques that not only provide a static intensity image of the biofilm, but also enable one to quantify various dynamic physicochemical properties of biomolecules in microbial biofilms. Such light microscopy-based techniques can be grouped into two main classes, those that are based on luminescence and those that are based on scattering. Here, we review the fundamentals and applications of luminescence and scattering-based techniques, specifically, fluorescence lifetime imaging, Förster resonance energy transfer, fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single-particle tracking, transient state imaging, and Brillouin and Raman microscopy. These techniques provide information about the abundance, interactions and mobility of various molecules in the biofilms and also properties of the local microenvironment at optical resolution. Further, one could use any of these techniques to probe the real-time changes in these physical parameters upon the addition of external agents or at different stages during the growth of biofilms.

Brillouin Light Scattering: Applications in Biomedical Sciences

Brillouin spectroscopy and imaging are emerging techniques in analytical science, biophotonics, and biomedicine. They are based on Brillouin light scattering from acoustic waves or phonons in the GHz range, providing a nondestructive contactless probe of the mechanics on a microscale. Novel approaches and applications of these techniques to the field of biomedical sciences are discussed, highlighting the theoretical foundations and experimental methods that have been developed to date. Acknowledging that this is a fast moving field, a comprehensive account of the relevant literature is critically assessed here.

Brillouin-Raman mapping of natural fibers with spectral moment analysis

Brillouin spectroscopy has emerged as a novel analytical tool for biophotonic research and applications. It operates on a microscopic scale and in the GHz spectral range, providing a new spatial and frequency window for the analysis of the materials elasticity. Here we investigate spectral moments calculation as a means of analysing Brillouin and Raman spectra, providing rapid access to peak intensity and frequency shift, with robust application to fast scanning measurements. This work demonstrates the potential of the method, especially in the case of micro-structured samples, typical of bio-medical applications.

Brillouin micro-spectroscopy through aberrations via sensorless adaptive optics

Brillouin spectroscopy is a powerful optical technique for non-contact viscoelastic characterizations which has recently found applications in three-dimensional mapping of biological samples. Brillouin spectroscopy performances are rapidly degraded by optical aberrations and have therefore been limited to homogenous transparent samples. In this work, we developed an adaptive optics (AO) configuration designed for Brillouin scattering spectroscopy to engineer the incident wavefront and correct for aberrations. Our configuration does not require direct wavefront sensing and the injection of a "guide-star"; hence, it can be implemented without the need for sample pre-treatment. We used our AO-Brillouin spectrometer in aberrated phantoms and biological samples and obtained improved precision and resolution of Brillouin spectral analysis; we demonstrated 2.5-fold enhancement in Brillouin signal strength and 1.4-fold improvement in axial resolution because of the correction of optical aberrations.

Yeast Biofilm as a Bridge Between Medical and Environmental Microbiology Across Different Detection Techniques

Medical and environmental microbiology have two distinct, although very short, histories stemming, the first from the pioneering works of Sommelweiss, Pasteur, Lister and Koch, the second mainly from the studies of Bejerink and Winogradsky. These two branches of microbiology evolved and specialized separately producing distinct communities and evolving rather different approaches and techniques. The evidence accumulated in recent decades indicate that indeed most of the medically relevant microorganisms have a short circulation within the nosocomial environment and a larger one involving the external, i.e. non-nosocomial, and the hospital environments. This evidence suggests that the differences between approaches should yield to a convergent approach aimed at solving the increasing problem represented by infectious diseases for the increasingly less resistant human communities. Microbial biofilm is one of the major systems used by these microbes to resist the harsh conditions of the natural and anthropic environment, and the even worse ones related to medical settings. This paper presents a brief outline of the converging interest of both environmental and medical microbiology toward a better understanding of microbial biofilm and of the various innovative techniques that can be employed to characterize, in a timely and quantitative manner, these complex structures. Among these, micro-Raman along with micro-Brillouin offer high hopes of describing biofilms both at the subcellular and supercellular level, with the possibility of characterizing the various landscapes of the different biofilms. The possibility of adding a taxonomic identification of the cells comprising the biofilm is a complex aspect presenting several technical issues that will require further studies in the years to come.

SIBPA under the Tuscan sun: Introduction to the SIBPA XXIII Special Issue

The Italian Society for Pure and Applied Biophysics (SIBPA) held its XXIII National Congress in the gorgeous Tuscan town of Cortona, Italy, on September 18-21, 2016. This special issue features a selection of contributions from the Congress in the areas of molecular, applied, cellular and computational biophysics. Cutting-edge developments in nanoscale biophysics were introduced for the first time in the program. SIBPA continues its successful promotion of biophysical disciplines at the national and international levels, with added strength from its partnership with Biophysical Chemistry and Elsevier.