Non-invasive methods of detecting radiation exposure show promise to improve upon current approaches to biological dosimetry in ease, speed, and accuracy. Here we developed a pipeline that employs Fourier transform infrared (FTIR) spectroscopy in the mid-infrared spectrum to identify a signature of low dose ionizing radiation exposure in mouse ear pinnae over time. Mice exposed to 0.1 to 2 Gy total body irradiation were repeatedly measured by FTIR at the stratum corneum of the ear pinnae. We found significant discriminative power for all doses and time-points out to 90 days after exposure. Classification accuracy was maximized when testing 14 days after exposure (specificity > 0.9 with a sensitivity threshold of 0.9) and dropped by roughly 30% sensitivity at 90 days. Infrared frequencies point towards biological changes in DNA conformation, lipid oxidation and accumulation and shifts in protein secondary structure. Since only hundreds of samples were used to learn the highly discriminative signature, developing human-relevant diagnostic capabilities is likely feasible and this non-invasive procedure points toward rapid, non-invasive, and reagent-free biodosimetry applications at population scales.

Surface enhanced infrared absorption (SEIRA) spectroscopy is a powerful tool in which plasmonically enhanced electromagnetic fields provide high-sensitivity molecular detection. Most SEIRA platforms operate at a single resonant frequency, which must be tuned to match that of the target molecule, and commonly rely on time-consuming lithographic techniques. This study presents a high-throughput and cost-effective plasmonic metasurface for broadband, tunable, and strong infrared signal enhancement. The platform is built upon the principle of dispersion-engineered plasmonic Fabry-Perot (FP) nanocavity arrays. It offers 1) tight squeezing of infrared (IR) photons into deep sub-wavelength nano-volumes and 2) spectrally tunable near-field enhancements of up to & AP;10(6), two to three orders of magnitude higher than most optical metasurface systems. By coupling multilayer nano-thin film deposition and nanoskiving fabrication techniques, the dispersive FP metasurfaces can be rapidly and reproducibly constructed in a scalable and lithography-free manner. Using IR spectroscopy, the selective and sensitive label-free detection of a molecular monolayer is achieved at a range of frequencies. An enhancement factor of nearly 10(5) is measured at the carbonyl (C = O) vibrational marker band of the molecule. The confluence of high field enhancement, broadband plasmonic response, and facile fabrication makes this metasurface a promising platform for SEIRA spectroscopy.

Soil drying challenges microbial viability and survival, with bacteria employing various mechanisms to respond to shifts in osmolarity, including dormancy or metabolic upregulation of osmoprotectants. However, the extent to which these responses are shaped by an organisms phylogeny or the climate history of a given environment is poorly understood. This study examines the responses of phylogenetically similar bacteria from semi-arid and humid tropical forest soils to osmotic and matric stress using synchrotron radiation-based Fourier Transform Infrared spectromicroscopy. This non-destructive approach depicts the biochemical phenotype for whole cells under control and stress conditions. We observed that, under osmotic stress, bacteria upregulated cell-signaling pathways, rapidly turned over lipid-storage compounds, and increased osmolyte production. In contrast, matric stress induced a more muted response, typically elevating the production of carbohydrate stress compounds, such as glycine betaine and trehalose. While phylogenetically similar bacteria showed comparable biochemistry under control conditions, climate history played an important role in regulating responses to stress, whereby a stronger metabolic response was observed from semi-arid relative to tropical forest isolates. We conclude that bacterial stress response to drought can be more diverse than previously observed, and regulated by both phylogeny and climate history. ### Competing Interest Statement The authors have declared no competing interest.

Spatial and temporal resolved mapping of infrared spectra of cellulose during enzymatic hydrolysis towards developing sustainable bioconversion processes to materials, fuels, and chemicals.

Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value lipid production. Yet much about their basic biology remains unknown, including the nature of an enigmatic, pigmented globule found in vegetative cells. Here, we present an in-depth examination of this "red body," focusing on Nannochloropsis oceanica. During the cell cycle, the red body forms adjacent to the plastid, but unexpectedly it is secreted and released with the autosporangial wall following cell division. Shed red bodies contain antioxidant ketocarotenoids, and overexpression of a beta-carotene ketolase results in enlarged red bodies. Infrared spectroscopy indicates long-chain, aliphatic lipids in shed red bodies and cell walls, and UHPLC-HRMS detects a C32 alkyl diol, a potential precursor of algaenan, a recalcitrant cell wall polymer. We propose that the red body transports algaenan precursors from plastid to apoplast to be incorporated into daughter cell walls.

Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.

Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value lipid production. Yet much about their basic biology remains unknown, including the nature of an enigmatic, pigmented globule found in vegetative cells. Here, we present an in-depth examination of this “red body”, focusing on Nannochloropsis oceanica . During the cell cycle, the red body formed adjacent to the plastid, but unexpectedly it was secreted and released with the autosporangial wall following cell division. Shed red bodies contained antioxidant ketocarotenoids, and overexpression of a beta-carotene ketolase resulted in enlarged red bodies. Infrared spectroscopy indicated long-chain, aliphatic lipids in shed red bodies and cell walls, and LC-HRMS detected a C32 alkyl diol, a potential precursor of algaenan, a recalcitrant cell wall polymer. We propose that the red body transports algaenan precursors from plastid to apoplast to be incorporated into daughter cell walls.

Well-defined aerosols pave the way for versatile basic and applied research. Here, we demonstrate a unique whipping instability that generates from a high-aspect-ratio microfluidic device resulting in a unique steady-state gas-focused whipping jet (WJ) without any need for electrification. This WJ device emanates a multi-monodisperse whipping spray jet with a two-dimensional (2D) profile. We demonstrate this phenomenon based on various fluidic parameters theoretically and experimentally. The 2D WJ’s unique behavior is derived using analytical fluid dynamics to explain jet diameter, whipping regime, and spreading angle. The phenomenon is further characterized experimentally by measuring the angle with respect to the flow rate, the distances between droplets, the droplet shapes, and the reproducibility of these parameters. We also explain the precise fabrication of such inexpensive devices. Lastly, we highlight these devices’ potential use as sample environments in versatile applications ranging from cryoelectron microscopy over mass spectrometry to drug formulation and structural studies at X-ray free-electron lasers.

<p>The frequency and intensity of environmental fluctuations play an important role in shaping microbial community composition, trait-distribution, and adaptive capacity. We hypothesize here that a communities’ climate history dictates it’s metabolic response to future perturbation under a changing climate. Such a response is significant as changes in microbial metabolism can, in turn, feedback onto metabolite exudation, the chemical structure of necromass, and the formation and stability of soil organic matter. Here we use laboratory and field experiments to examine the metabolic pathways invoked under osmotic and matric stress within semi-arid and tropical soils. For example, using non-destructive, synchrotron-based Fourier-transform infrared spectromicroscopy we profiled the stress response of phylogenetically similar bacteria isolated from soils with contrasting climate histories subjected to both matric and osmotic stress. We note a strong carbohydrate-based, metabolic response of tropical microbes that is entirely absent in semi-arid organisms. At the field scale, we use metagenomic sequencing and metabolite analysis to demonstrate how four different sites established across a 1 m precipitation gradient from the Caribbean coast to the interior of Panama respond to a 50 % reduction in throughfall. The precipitation gradient permits the development of distinct communities at each site that show clearly divergent response to imposed hydrological perturbation. Our contribution here will discuss how communities adapted to different precipitation regimes respond metabolically to drought conditions, and how these change feedback onto the structure and stability of soil organic matter.    </p>

Cesium (Cs + ) enters environments largely because of global release into the environment from weapons testing and accidents such as Fukushima Daiichi and Chernobyl nuclear waste. Even at low concentrations, Cs + is highly toxic to ecological receptors because of its physicochemical similarity to macronutrient potassium (K + ). We investigated the uptake and accumulation of Cs + by Arthrobacter globiformis strain 151B in reference to three similar alkali metal cations rubidium (Rb + ), sodium (Na + ), and potassium (K + ). The impact of hexavalent chromium (Cr +6 ) as a co-contaminant was also evaluated. A. globiformis 151B accumulated Cs + and Cr 6+ in a time-dependent fashion. In contrast, the uptake and accumulation of Rb + did not exhibit any trends. An exposure to Cs + , Rb + , and Cr +6 triggered a drastic increase in K + and Na + uptake by the bacterial cells. That was followed by the efflux of K + and Na + , suggesting a Cs + “substitution.” Two-dimensional gel-electrophoresis of bacterial cell proteomes with the following mass-spectrometry of differentially expressed bands revealed that incubation of bacterial cells with Cs + induced changes in the expression of proteins involved in the maintenance of cellular homeostasis and reactive oxygen species removal. The ability of A. globiformis 151B to mediate the uptake and accumulation of cesium and hexavalent chromium suggests that it possesses wide-range bioremediation potential.

High-density microfluidics is becoming an important experimental platform for studying complex biological systems such as synthetic gene regulatory networks, molecular biocomputating of engineered cells, distributing rapid point-of-care diagnosis, and monitoring pathological environment. Imaging transient bio-chemical reactions happening in these systems at a single particle or cellular level requires precise time-dependent control of sample reaction and imaging conditions at the desired fluidic momentum. In this study, we showed our novel miniaturized and programmable electronic-based pneumatic system to meet the requirement. We demonstrated its capability to control reaction parameters such as concentrations and injection rates in a liposome production system.

Author(s): Holman, Hoi Ying N; Zhao, Wujun; Nill, Jennifer; Chen, Liang; Narayanasamy, Sankar Raju; Jeoh, Tina | Abstract: Synchrotron infrared hyperspectral microscopy is a label-free and non-invasive technique well suited for imaging of chemical events in situ. It can track the spatial and temporal distributions of molecules of interests in a specimen in its native state by the molecule’s characteristic vibrational modes. Despite tremendous progress made in recent years, IR hyperspectral imaging of chemical events in biomaterials in liquids remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. Here we report a multi-phase capillary-driven membrane device for label-free and real-time investigation of enzymatic deconstruction of algal cellulose purified from Cladophora aegagropila.

The execution and analysis of complex experiments are challenged by the vast dimensionality of the underlying parameter spaces. Although an increase in data-acquisition rates should allow broader querying of the parameter space, the complexity of experiments and the subtle dependence of the model function on input parameters remains daunting owing to the sheer number of variables. New strategies for autonomous data acquisition are being developed, with one promising direction being the use of Gaussian process regression (GPR). GPR is a quick, non-parametric and robust approximation and uncertainty quantification method that can be applied directly to autonomous data acquisition. We review GPR-driven autonomous experimentation and illustrate its functionality using real-world examples from large experimental facilities in the USA and France. We introduce the basics of a GPR-driven autonomous loop with a focus on Gaussian processes, and then shift the focus to the infrastructure that needs to be built around GPR to create a closed loop. Finally, the case studies we discuss show that Gaussian-process-based autonomous data acquisition is a widely applicable method that can facilitate the optimal use of instruments and facilities by enabling the efficient acquisition of high-value datasets. Gaussian process regression (GPR) is a powerful, non-parametric and robust technique for uncertainty quantification and function approximation that can be applied to optimal and autonomous data acquisition. This Review introduces the basics of GPR and discusses several use cases from different fields.

Synchrotron infrared hyperspectral microscopy is a label-free and non-invasive technique well suited for imaging of chemical events in situ. It can track the spatial and temporal distributions of molecules of interests in a specimen in its native state by the molecule's characteristic vibrational modes. Despite tremendous progress made in recent years, IR hyperspectral imaging of chemical events in biomaterials in liquids remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. Here we report a multi-phase capillary-driven membrane device for label-free and real-time investigation of enzymatic deconstruction of algal cellulose purified from Cladophora aegagropila.

Infrared (IR) absorption spectromicroscopy is a powerful, non-invasive probe that provides access to spatio-chemical information at the micron scale. The physical basis of IR spectroscopy lies in the oscillations of dynamic dipole moments in chemical bonds, with resonant frequencies in the IR spectral region of 4,000-400 cm -1 wave numbers. The bending or stretching of chemical bonds between atoms with different electronegativities, such as O-H or C=O, will lead to intense absorption and thus provide a unique fingerprint of specific chemical groups within the sample. The presence - or absence - of specific spectral fingerprints provide the opportunity to locate and identify chemical processes throughout the sample and track these processes in time or as a function of external perturbation. We can perform these types of measurements using a Synchrotron Fourier Transform Infrared (SFTIR) spectromicroscopy setup, as it provides orders of magnitude more photons than traditional bench-top machines 1 . Even with an ultra-bright IR source as provided at the Advanced Light Source, acquisition times typically take multiple hours. These long acquisition times are in part caused by the size of the field of view, as compared to the probe size: users typically analyze a 70 um by 100 um sample using a regular grid with a spacing of 1 um. With an acquisition time of 4 seconds per pixel, we would need about 8 hours to measure the full sample. Given that access to instruments is scarce, compounded by the desire to characterize different samples, being able to speed up data acquisition is of paramount importance. Here we present a strategy that drastically increases the efficiency of SFTIR spectromicroscopy by coupling the data collection with Gaussian Process based surrogate model 2,3 . This approach models the full hyperspectral datasets across the entire field of view, including regions we haven’t measure d yet, by multivariate Normal distribution. By analyzing this distribution, we gain insight into which future measurement locations provide the greatest reduction in total uncertainty and can also predict various quality metrics of the surrogate model we can use to end an experiment. Preliminary experiments show we can increase the throughput of SFTIR experiments by a factor of ~20.

Model projections predict that climate change impacts on the tropics will include an increased frequency of drought and precipitation cycles. Such environmental fluctuations at the soil pore-scale play an important role in shaping microbial adaptive capacity, and trait composition of a community, which feeds back on to the breakdown and formation of soil organic matter (SOM). Understanding the factors controlling the carbon balance of humid tropical forest soils remains a social imperative. Microbial feedback to SOM pools is critical. Herein, we examine the microbial response to drought perturbations across 3 different, but complementary scales. At the largest scale, we explored the impacts of drought across a 1 m precipitation gradient spanning four sites from the Caribbean coast to the interior of Panama. At each site 4, throughfall exclusion plots (10 x 10 m) were established to reduce precipitation by 50 %. In addition, 4 corresponding control plots were also constructed. At the meso-scale, we incubated intact soil cores from one of these sites (P12) under 3 different hydrological treatments (control, drought, rewetting-drying cycles) for over a 5-month period. For the field and meso-scale experiments, we evaluated changes imparted by hydrological perturbations using multi-omic approaches, and physico-chemical measurements. In order to identify the traits involved in response to drought at the field and meso-scale, we isolated a range of bacteria to subject to stress at the scale of the single-cell and simple communities. Cell extracts were subjected to osmotic or matric stress and the short-term physiological responses determined using non-destructive synchrotron radiation-based Fourier Transform-Infrared spectromicroscopy. Through this approach, we identified changes in metabolic allocation within different cells, in particular to the secondary metabolome of the different bacteria. Our contribution will discuss the outcomes of these multi-scale experiments. Specifically focusing on how shifts in the microbial community and physiological changes may influence tropical soil carbon stability under future scenarios of altered drought and precipitation cycles.