In vivo hyperspectral confocal fluorescence imaging to determine pigment localization and distribution in cyanobacterial cells

Archaean green-light environments drove the evolution of cyanobacteria's light-harvesting system

Cyanobacteria induced the great oxidation event around 2.4 billion years ago, probably triggering the rise in aerobic biodiversity. While chlorophylls are universal pigments used by all phototrophic organisms, cyanobacteria use additional pigments called phycobilins for their light-harvesting antennas-phycobilisomes-to absorb light energy at complementary wavelengths to chlorophylls. Nonetheless, an enigma persists: why did cyanobacteria need phycobilisomes? Here, we demonstrate through numerical simulations that the underwater light spectrum during the Archaean era was probably predominantly green owing to oxidized Fe(III) precipitation. The green-light environments, probably shaped by photosynthetic organisms, may have directed their own photosynthetic evolution. Genetic engineering of extant cyanobacteria, simulating past natural selection, suggests that cyanobacteria that acquired a green-specialized phycobilin called phycoerythrobilin could have flourished under green-light environments. Phylogenetic analyses indicate that the common ancestor of modern cyanobacteria embraced all key components of phycobilisomes to establish an intricate energy transfer mechanism towards chlorophylls using green light and thus gained strong selective advantage under green-light conditions. Our findings highlight the co-evolutionary relationship between oxygenic phototrophs and light environments that defined the aquatic landscape of the Archaean Earth and envision the green colour as a sign of the distinct evolutionary stage of inhabited planets.

Methodological challenges for the investigation of the dual role of biofilms on outdoor heritage

Biofilm deterioration and biofilm protection should be considered as different aspects of the complex interactions between microbes and the surfaces of outdoor heritage (e.g. stones, bricks, mortar and plaster). Thus, it is urgent to verify and quantify to what extent the biofilm can protect from different weathering processes, to eventually determine the advisability of biofilm removal from the heritage surfaces. On one hand, it is necessary to more precisely describe the decaying processes caused by the microorganisms and to quantify the extent, severity, and rate at which the microorganisms are causing the decay. On the other hand, it is necessary to define methodologies to comprehensively study the bioprotection phenomena. So far, no decision-making tool is available to guide heritage professionals in deciding whether to remove or keep biofilms on heritage surfaces, and aesthetical alteration and discoloration is often the only criterion considered. In this work the different available approaches for the study of the dual role of biofilms on outdoor heritage have been critically reviewed. The open challenges and questions are also summarised.

Implicating the red body of Nannochloropsis in forming the recalcitrant cell wall polymer algaenan

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.

Functional consequences of modification of the photosystem I/photosystem II ratio in the cyanobacterium Synechocystis sp. PCC 6803

The stoichiometry of photosystem II (PSII) and photosystem I (PSI) varies between photoautotrophic organisms. The cyanobacterium Synechocystis sp. PCC 6803 maintains two- to fivefold more PSI than PSII reaction center complexes, and we sought to modify this stoichiometry by changing the promoter region of the psaAB operon. We thus generated mutants with varied psaAB expression, ranging from ~3% to almost 200% of the wild-type transcript level, but all showing a reduction in PSI levels, relative to wild type, suggesting a role of the psaAB promoter region in translational regulation. Mutants with 25%-70% of wild-type PSI levels were photoautotrophic, with whole-chain oxygen evolution rates on a per-cell basis comparable to that of wild type. In contrast, mutant strains with <10% of the wild-type level of PSI were obligate photoheterotrophs. Variable fluorescence yields of all mutants were much higher than those of wild type, indicating that the PSI content is localized differently than in wild type, with less transfer of PSII-absorbed energy to PSI. Strains with less PSI saturate at a higher light intensity, enhancing productivity at higher light intensities. This is similar to what is found in mutants with reduced antennae. With 3-(3,4-dichlorophenyl)-1,1-dimethylurea present, P700+ re-reduction kinetics in the mutants were slower than in wild type, consistent with the notion that there is less cyclic electron transport if less PSI is present. Overall, strains with a reduction in PSI content displayed surprisingly vigorous growth and linear electron transport.

IMPORTANCE

Consequences of reduction in photosystem I content were investigated in the cyanobacterium Synechocystis sp. PCC 6803 where photosystem I far exceeds the number of photosystem II complexes. Strains with less photosystem I displayed less cyclic electron transport, grew more slowly at lower light intensity and needed more light for saturation but were surprisingly normal in their whole-chain electron transport rates, implying that a significant fraction of photosystem I is dispensable for linear electron transport in cyanobacteria. These strains with reduced photosystem I levels may have biotechnological relevance as they grow well at higher light intensities.

Deep learning-enhanced snapshot hyperspectral confocal microscopy imaging system

Laser-scanning confocal hyperspectral microscopy is a powerful technique to identify the different sample constituents and their spatial distribution in three-dimensional (3D). However, it suffers from low imaging speed because of the mechanical scanning methods. To overcome this challenge, we propose a snapshot hyperspectral confocal microscopy imaging system (SHCMS). It combined coded illumination microscopy based on a digital micromirror device (DMD) with a snapshot hyperspectral confocal neural network (SHCNet) to realize single-shot confocal hyperspectral imaging. With SHCMS, high-contrast 160-bands confocal hyperspectral images of potato tuber autofluorescence can be collected by only single-shot, which is almost 5 times improvement in the number of spectral channels than previously reported methods. Moreover, our approach can efficiently record hyperspectral volumetric imaging due to the optical sectioning capability. This fast high-resolution hyperspectral imaging method may pave the way for real-time highly multiplexed biological imaging.

Microdomains heterogeneity in the thylakoid membrane proteins visualized by super-resolution microscopy

The investigation of spatial heterogeneity within the thylakoid membrane (TM) proteins has gained increasing attention in photosynthetic research. The recent advances in live-cell imaging have allowed the identification of heterogeneous organisation of photosystems in small cyanobacterial cells. These sub-micrometre TM regions, termed microdomains in cyanobacteria, exhibit functional similarities with granal (Photosystem II dominant) and stromal (Photosystem I dominant) regions observed in TM of higher plants. This study delves into microdomain heterogeneity using super-resolution Airyscan-based microscopy enhancing resolution to approximately ~125 nm in x-y dimension. The new data reveal membrane areas rich in Photosystem I within the inner TM rings. Moreover, we identified analogous dynamics in the mobility of Photosystem II and phycobilisomes; countering earlier models that postulated differing mobility of these complexes. These novel findings thus hold significance for our understanding of photosynthesis regulation, particularly during state transitions.

Development status of novel spectral imaging techniques and application to traditional Chinese medicine

Traditional Chinese medicine (TCM) is a treasure of the Chinese nation, providing effective solutions to current medical requisites. Various spectral techniques are undergoing continuous development and provide new and reliable means for evaluating the efficacy and quality of TCM. Because spectral techniques are noninvasive, convenient, and sensitive, they have been widely applied to in vitro and in vivo TCM evaluation systems. In this paper, previous achievements and current progress in the research on spectral technologies (including fluorescence spectroscopy, photoacoustic imaging, infrared thermal imaging, laser-induced breakdown spectroscopy, hyperspectral imaging, and surface enhanced Raman spectroscopy) are discussed. The advantages and disadvantages of each technology are also presented. Moreover, the future applications of spectral imaging to identify the origins, components, and pesticide residues of TCM in vitro are elucidated. Subsequently, the evaluation of the efficacy of TCM in vivo is presented. Identifying future applications of spectral imaging is anticipated to promote medical research as well as scientific and technological explorations.

Scytonemin redox status in a filamentous cyanobacterium visualized by an excitation-laser-line-scanning spontaneous Raman scattering spectral microscope

Some cyanobacteria produce a UVA-absorbing pigment, scytonemin, at extracellular sheaths. Although scytonemin-containing dark sheaths are recognizable through optical microscopes and its redox changes have been known for decades, there has been no report to obtain images of both oxidized and reduced scytonemins at subcellular resolution. Here, we show that a spontaneous Raman scattering spectral microscopy based on an excitation-laser-line-scanning method unveil 3D subcellular distributions of both the oxidized and reduced scytonemins in a filamentous cyanobacterium. The redox changes of scytonemin were supported by comparison in the Raman spectra between the cyanobacterial cells, solid-state scytonemin and quantum chemical normal mode analysis. Distributions of carotenoids, phycobilins, and the two redox forms of scytonemin were simultaneously visualized with an excitation wavelength at 1064 nm that is virtually free from the optical screening by the dark sheaths. The redox differentiation of scytonemin will advance our understanding of the redox homeostasis and secretion mechanisms of individual cyanobacteria as well as microscopic chemical environments in various microbial communities. The line-scanning Raman microscopy based on the 1064 nm excitation is thus a promising tool for exploring hitherto unreported Raman spectral features and distribution of nonfluorescent molecules embedded below nontransparent layers for visible light, while avoiding interference by autofluorescence.

Compact and ultracompact spectral imagers: technology and applications in biomedical imaging

Significance

Spectral imaging, which includes hyperspectral and multispectral imaging, can provide images in numerous wavelength bands within and beyond the visible light spectrum. Emerging technologies that enable compact, portable spectral imaging cameras can facilitate new applications in biomedical imaging.

Aim

With this review paper, researchers will (1) understand the technological trends of upcoming spectral cameras, (2) understand new specific applications that portable spectral imaging unlocked, and (3) evaluate proper spectral imaging systems for their specific applications.

Approach

We performed a comprehensive literature review in three databases (Scopus, PubMed, and Web of Science). We included only fully realized systems with definable dimensions. To best accommodate many different definitions of "compact," we included a table of dimensions and weights for systems that met our definition.

Results

There is a wide variety of contributions from industry, academic, and hobbyist spaces. A variety of new engineering approaches, such as Fabry-Perot interferometers, spectrally resolved detector array (mosaic array), microelectro-mechanical systems, 3D printing, light-emitting diodes, and smartphones, were used in the construction of compact spectral imaging cameras. In bioimaging applications, these compact devices were used for in vivo and ex vivo diagnosis and surgical settings.

Conclusions

Compact and ultracompact spectral imagers are the future of spectral imaging systems. Researchers in the bioimaging fields are building systems that are low-cost, fast in acquisition time, and mobile enough to be handheld.

Flexible hyperspectral surface plasmon resonance microscopy

Optical techniques for visualization and quantification of chemical and biological analytes are always highly desirable. Here we show a hyperspectral surface plasmon resonance microscopy (HSPRM) system that uses a hyperspectral microscope to analyze the selected area of SPR image produced by a prism-based spectral SPR sensor. The HSPRM system enables monochromatic and polychromatic SPR imaging and single-pixel spectral SPR sensing, as well as two-dimensional quantification of thin films with the measured resonance-wavelength images. We performed pixel-by-pixel calibration of the incident angle to remove pixel-to-pixel differences in SPR sensitivity, and demonstrated the HSPRM's capabilities by using it to quantify monolayer graphene thickness distribution, inhomogeneous protein adsorption and single-cell adhesion. The HSPRM system has a wide spectral range from 400 nm to 1000 nm, an optional field of view from 0.884 mm² to 0.003 mm² and a high lateral resolution of 1.2 μm, demonstrating an innovative breakthrough in SPR sensor technology.

Microscopy is better in color: development of a streamlined spectral light path for real-time multiplex fluorescence microscopy

Spectroscopic image data has provided molecular discrimination for numerous fields including: remote sensing, food safety and biomedical imaging. Despite the various technologies for acquiring spectral data, there remains a trade-off when acquiring data. Typically, spectral imaging either requires long acquisition times to collect an image stack with high spectral specificity or acquisition times are shortened at the expense of fewer spectral bands or reduced spatial sampling. Hence, new spectral imaging microscope platforms are needed to help mitigate these limitations. Fluorescence excitation-scanning spectral imaging is one such new technology, which allows more of the emitted signal to be detected than comparable emission-scanning spectral imaging systems. Here, we have developed a new optical geometry that provides spectral illumination for use in excitation-scanning spectral imaging microscope systems. This was accomplished using a wavelength-specific LED array to acquire spectral image data. Feasibility of the LED-based spectral illuminator was evaluated through simulation and benchtop testing and assessment of imaging performance when integrated with a widefield fluorescence microscope. Ray tracing simulations (TracePro) were used to determine optimal optical component selection and geometry. Spectral imaging feasibility was evaluated using a series of 6-label fluorescent slides. The LED-based system response was compared to a previously tested thin-film tunable filter (TFTF)-based system. Spectral unmixing successfully discriminated all fluorescent components in spectral image data acquired from both the LED and TFTF systems. Therefore, the LED-based spectral illuminator provided spectral image data sets with comparable information content so as to allow identification of each fluorescent component. These results provide proof-of-principle demonstration of the ability to combine output from many discrete wavelength LED sources using a double-mirror (Cassegrain style) optical configuration that can be further modified to allow for high speed, video-rate spectral image acquisition. Real-time spectral fluorescence microscopy would allow monitoring of rapid cell signaling processes (i.e., Ca2+ and other second messenger signaling) and has potential to be translated to clinical imaging platforms.

Leaf microscopy applications in photosynthesis research: identifying the gaps

Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure-function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.

Acclimation response and ability of growth and photosynthesis of terrestrial cyanobacterium Cylindrospermum sp. strain FS 64 under combined environmental factors

This investigation tested the hypothesis that the native cyanobacteria can acclimatize and grow under the combination of environmental factors and/or how does their process change with the age of culture? Here, we tried to combine multiple factors to simulated what happens in natural ecosystems. We analyzed the physiological response of terrestrial cyanobacterium, Cylindrospermum sp. FS 64 under combination effect of different salinity (17, 80, and 160 mM) and alkaline pHs (9 and 11) at extremely limited carbon dioxide concentration (no aeration) up to 96 h. Our evidence showed that growth, biomass, photosystem II, and phycobilisome activity significantly increased under 80 mM salinity and pH 11. In addition, this combined condition led to a significant increase in maximum light-saturated photosynthesis activity and photosynthetic efficiency. While phycobilisomes and photosystem activity decreased by increasing salinity (160 mM) which caused decreased growth rates after 96 h. The single-cell study (CLMS microscopy) which illustrated the physiological state of the individual and active-cell confirmed the efficiency and effectiveness of both photosystems and phycobilisome under the combined effect of 80 mM salinity and pH 11.

Growth and photosynthesis acclimated response of the cyanobacterium Fischerella sp. FS 18 exposed to extreme conditions: alkaline pH, limited irradiance, and carbon dioxide concentration

The true-branching heterocystous cyanobacterium Fischerella sp. FS 18 is widely distributed in paddy fields (North) and petroleum polluted soils (South) in Iran. This investigation tested the hypothesis that the cyanobacterium can acclimatize under the combined effect of extreme environmental conditions. Here, we analysed the physiological response of the cyanobacterium under extremely limited irradiance (2 μmol photon m^-2 s^-1); limited carbon dioxide concentration (no aeration) at alkaline pHs (9 and 11) for up to 96 h. When the cyanobacterium was exposed to these extreme conditions at pH 11, we observed a decline in growth, oxygen liberation, photosystems ratio, chlorophyll a, and phycobilisomes activity compared to pH 9 after 24 h. Besides, we registered a significant decrease in maximum photochemical efficiency and activity of photosystem II at pH 11. The comparative single-cell study revealed that pH 9 caused higher efficiency of photosystem II and I, while increasing alkalinity pH 11 led to disturbed phycobilisomes activity after 24 h. This strain was able to recover its structures after 96 h. In addition, spectroscopy analyses revealed the presence of the Mycosporine-like amino acid at pH 9.

Gradual Response of Cyanobacterial Thylakoids to Acute High-Light Stress-Importance of Carotenoid Accumulation

Light plays an essential role in photosynthesis; however, its excess can cause damage to cellular components. Photosynthetic organisms thus developed a set of photoprotective mechanisms (e.g., non-photochemical quenching, photoinhibition) that can be studied by a classic biochemical and biophysical methods in cell suspension. Here, we combined these bulk methods with single-cell identification of microdomains in thylakoid membrane during high-light (HL) stress. We used Synechocystis sp. PCC 6803 cells with YFP tagged photosystem I. The single-cell data pointed to a three-phase response of cells to acute HL stress. We defined: (1) fast response phase (0–30 min), (2) intermediate phase (30–120 min), and (3) slow acclimation phase (120–360 min). During the first phase, cyanobacterial cells activated photoprotective mechanisms such as photoinhibition and non-photochemical quenching. Later on (during the second phase), we temporarily observed functional decoupling of phycobilisomes and sustained monomerization of photosystem II dimer. Simultaneously, cells also initiated accumulation of carotenoids, especially ɣ–carotene, the main precursor of all carotenoids. In the last phase, in addition to ɣ-carotene, we also observed accumulation of myxoxanthophyll and more even spatial distribution of photosystems and phycobilisomes between microdomains. We suggest that the overall carotenoid increase during HL stress could be involved either in the direct photoprotection (e.g., in ROS scavenging) and/or could play an additional role in maintaining optimal distribution of photosystems in thylakoid membrane to attain efficient photoprotection.

State transitions and photosystems spatially resolved in individual cells of the cyanobacterium Synechococcus elongatus

State transitions are a low-light acclimation response through which the excitation of Photosystem I (PSI) and Photosystem II (PSII) is balanced; however, our understanding of this process in cyanobacteria remains poor. Here, picosecond fluorescence kinetics was recorded for the cyanobacterium Synechococcus elongatus using fluorescence lifetime imaging microscopy (FLIM), both upon chlorophyll a and phycobilisome (PBS) excitation. Fluorescence kinetics of single cells obtained using FLIM were compared with those of ensembles of cells obtained with time-resolved fluorescence spectroscopy. The global distribution of PSI and PSII and PBSs was mapped making use of their fluorescence kinetics. Both radial and lateral heterogeneity were found in the distribution of the photosystems. State transitions were studied at the level of single cells. FLIM results show that PSII quenching occurs in all cells, irrespective of their state (I or II). In S. elongatus cells, this quenching is enhanced in State II. Furthermore, the decrease of PSII fluorescence in State II was homogeneous throughout the cells, despite the inhomogeneous PSI/PSII ratio. Finally, some disconnected PBSs were resolved in most State II cells. Taken together our data show that PSI is enriched in the inner thylakoid, while state transitions occur homogeneously throughout the cell.

Snapshot spectroscopic microscopy with double spherical slicer mirrors

Snapshot hyperspectral microscopic imaging can obtain the morphological characteristics and chemical specificity of samples simultaneously and instantaneously. We demonstrate a double-slicer spectroscopic microscopy (DSSM) that uses two spherical slicer mirrors to magnify the target image and slice it. These slits are lined up and dispersed, then mapped onto an area-array detector. An anamorphosis unit optimizes the capacity of the limited pixels. With a single shot and image recombination, a data cube can be constructed for sample analysis, and a model of DSSM is simulated. The system covers the spectral range from 500 nm to 642.5 nm with 20 spectral channels. The spatial resolution is 417 nm, and the spectral resolution is 7.5 nm.

Membrane Dynamics in Phototrophic Bacteria

Photosynthetic membranes are typically densely packed with proteins, and this is crucial for their function in efficient trapping of light energy. Despite being crowded with protein, the membranes are fluid systems in which proteins and smaller molecules can diffuse. Fluidity is also crucial for photosynthetic function, as it is essential for biogenesis, electron transport, and protein redistribution for functional regulation. All photosynthetic membranes seem to maintain a delicate balance between crowding, order, and fluidity. How does this work in phototrophic bacteria? In this review, we focus on two types of intensively studied bacterial photosynthetic membranes: the chromatophore membranes of purple bacteria and the thylakoid membranes of cyanobacteria. Both systems are distinct from the plasma membrane, and both have a distinctive protein composition that reflects their specialized roles. Chromatophores are formed from plasma membrane invaginations, while thylakoid membranes appear to be an independent intracellular membrane system. We discuss the techniques that can be applied to study the organization and dynamics of these membrane systems, including electron microscopy techniques, atomic force microscopy, and many variants of fluorescence microscopy. We go on to discuss the insights that havebeen acquired from these techniques, and the role of membrane dynamics in the physiology of photosynthetic membranes. Membrane dynamics on multiple timescales are crucial for membrane function, from electron transport on timescales of microseconds to milliseconds to regulation and biogenesis on timescales of minutes to hours. We emphasize the open questions that remain in the field.

Dark-field hyperspectral imaging for label free detection of nano-bio-materials

Nanomaterials are playing an increasingly important role in cancer diagnosis and treatment. Nanoparticle (NP)-based technologies have been utilized for targeted drug delivery during chemotherapies, photodynamic therapy, and immunotherapy. Another active area of research is the toxicity studies of these nanomaterials to understand the cellular uptake and transport of these materials in cells, tissues, and environment. Traditional techniques such as transmission electron microscopy, and mass spectrometry to analyze NP-based cellular transport or toxicity effect are expensive, require extensive sample preparation, and are low-throughput. Dark-field hyperspectral imaging (DF-HSI), an integration of spectroscopy and microscopy/imaging, provides the ability to investigate cellular transport of these NPs and to quantify the distribution of them within bio-materials. DF-HSI also offers versatility in non-invasively monitoring microorganisms, single cell, and proteins. DF-HSI is a low-cost, label-free technique that is minimally invasive and is a viable choice for obtaining high-throughput quantitative molecular analyses. Multimodal imaging modalities such as Fourier transform infrared and Raman spectroscopy are also being integrated with HSI systems to enable chemical imaging of the samples. HSI technology is being applied in surgeries to obtain molecular information about the tissues in real-time. This article provides brief overview of fundamental principles of DF-HSI and its application for nanomaterials, protein-detection, single-cell analysis, microbiology, surgical procedures along with technical challenges and future integrative approach with other imaging and measurement modalities. This article is categorized under: Diagnostic Tools > in vitro Nanoparticle-Based Sensing Diagnostic Tools > in vivo Nanodiagnostics and Imaging Implantable Materials and Surgical Technologies > Nanoscale Tools and Techniques in Surgery.

Programmable hyperspectral microscopy for high-contrast biomedical imaging in a snapshot

SIGNIFICANCE

Hyperspectral microscopy has been intensively explored in biomedical applications. However, due to its huge three-dimensional hyperspectral data cube, it typically suffers from slow data acquisition, mass data transmission and storage, and computationally expensive postprocessing.

AIM

To overcome the above limitations, a programmable hyperspectral microscopy technique was developed, which can perform hardware-based hyperspectral data postprocessing by the physical process of optical imaging in a snapshot.

APPROACH

A programmable hyperspectral microscopy system was developed to collect coded microscopic images from samples under multiplexed illumination. Principal component analysis followed by linear discriminant analysis scheme was coded into multiplexed illumination and realized by the physical process of optical imaging. The contrast enhancement was evaluated on two representative types of microscopic samples, i.e., tissue section and cell samples.

RESULTS

Compared to the microscopic images collected under white light illumination, the contrasts of coded microscopic images were significantly improved by 41% and 59% for tissue section and cell samples, respectively.

CONCLUSIONS

The proposed method can perform hyperspectral data acquisition and postprocessing simultaneously by its physical process, while preserving the most important spectral information to maximize the difference between the target and background, thus opening a new avenue for high-contrast microscopic imaging in a snapshot.

Formation and Preservation of Microbial Palisade Fabric in Silica Deposits from El Tatio, Chile

Palisade fabric is a ubiquitous texture of silica sinter found in low temperature (<40°C) regimes of hot spring environments, and it is formed when populations of filamentous microorganisms act as templates for silica polymerization. Although it is known that postdepositional processes such as biological degradation and dewatering can strongly affect preservation of these fabrics, the impact of extreme aridity has so far not been studied in detail. Here, we report a detailed analysis of recently silicified palisade fabrics from a geyser in El Tatio, Chile, tracing the progressive degradation of microorganisms within the silica matrix. This is complemented by heating experiments of natural sinter samples to assess the role of diagenesis. Sheathed cyanobacteria, identified as Leptolyngbya sp., were found to be incorporated into silica sinter by irregular cycles of wetting, evaporation, and mineral precipitation. Transmission electron microscopy analyses revealed that nanometer-sized silica particles are filling the pore space within individual cyanobacterial sheaths, giving rise to their structural rigidity to sustain a palisade fabric framework. Diagenesis experiments further show that the sheaths of the filaments are preferentially preserved relative to the trichomes, and that the amount of water present within the sinter is an important factor for overall preservation during burial. This study confirms that palisade fabrics are efficiently generated in a highly evaporative geothermal field, and that these biosignatures can be most effectively preserved under dry diagenetic conditions.

Revisiting cyanobacterial state transitions

Critical evaluation of “new” and “old” models of cyanobacterial state transitions. Phycobilisome and membrane contributions to this mechanism are addressed. The signaling transduction pathway is discussed.

Development of a Multicolor Line-Focus Microscope for Rapid Acquisitions of Excitation Spectra

To conduct rapid microscope observations with the excitation spectral measurement for photosynthetic organisms, a wavelength-dispersive line-focus microscope was developed. In the developed system, fluorescence signals at multiple positions on a sample excited with different wavelengths can be detected as a two-dimensional image on the EMCCD camera at the same time. Using the developed system, one can obtain excitation spectra at every pixel over the excitation wavelength range from 635 to 695 nm, which covers the full range of the Q_y bands of both chlorophyll-a and chlorophyll-b. Recording the reference laser spectra at the same time ensures robust measurement against the moderate spectral fluctuation in the excitation laser. Using an objective lens with a numerical aperture of 0.9, the lateral and axial resolutions of 0.56 and 1.08 μm, respectively, were achieved. The theoretically limited and experimentally estimated spectral resolutions of the excitation spectral measurement were 0.86 and 1.3 nm, respectively. The validity of the system was demonstrated by measuring fluorescent beads and single cells of a model alga, Chlamydomonas reinhardtii. Intrachloroplast inhomogeneity in the relative intensity of the chlorophyll-b band could be visualized in Chlamydomonas cells. The inhomogeneity reflects the intrachloroplast variation in the local peripheral antenna size.

Cellular localization of tolyporphins, unusual tetrapyrroles, in a microbial photosynthetic community determined using hyperspectral confocal fluorescence microscopy

The cyanobacterial culture HT-58-2, composed of a filamentous cyanobacterium and accompanying community bacteria, produces chlorophyll a as well as the tetrapyrrole macrocycles known as tolyporphins. Almost all known tolyporphins (A-M except K) contain a dioxobacteriochlorin chromophore and exhibit an absorption spectrum somewhat similar to that of chlorophyll a. Here, hyperspectral confocal fluorescence microscopy was employed to noninvasively probe the locale of tolyporphins within live cells under various growth conditions (media, illumination, culture age). Cultures grown in nitrate-depleted media (BG-11₀ vs. nitrate-rich, BG-11) are known to increase the production of tolyporphins by orders of magnitude (rivaling that of chlorophyll a) over a period of 30-45 days. Multivariate curve resolution (MCR) was applied to an image set containing images from each condition to obtain pure component spectra of the endogenous pigments. The relative abundances of these components were then calculated for individual pixels in each image in the entire set, and 3D-volume renderings were obtained. At 30 days in media with or without nitrate, the chlorophyll a and phycobilisomes (combined phycocyanin and phycobilin components) co-localize in the filament outer cytoplasmic region. Tolyporphins localize in a distinct peripheral pattern in cells grown in BG-11₀ versus a diffuse pattern (mimicking the chlorophyll a localization) upon growth in BG-11. In BG-11₀, distinct puncta of tolyporphins were commonly found at the septa between cells and at the end of filaments. This work quantifies the relative abundance and envelope localization of tolyporphins in single cells, and illustrates the ability to identify novel tetrapyrroles in the presence of chlorophyll a in a photosynthetic microorganism within a non-axenic culture.

Function of the IsiA pigment-protein complex in vivo

The acclimation of cyanobacterial photosynthetic apparatus to iron deficiency is crucial for their performance under limiting conditions. In many cyanobacterial species, one of the major responses to iron deficiency is the induction of isiA. The function of the IsiA pigment-protein complex has been the subject of intensive research. In this study of the model Synechocystis sp. PCC 6803 strain, we probe the accumulation of the pigment-protein complex and its effects on in vivo photosynthetic performance. We provide evidence that in this organism the dominant factor controlling IsiA accumulation is the intracellular iron concentration and not photo-oxidative stress or redox poise. These findings support the use of IsiA as a tool for assessing iron bioavailability in environmental studies. We also present evidence demonstrating that the IsiA pigment-protein complex exerts only small effects on the performance of the reaction centers. We propose that its major function is as a storage depot able to hold up to 50% of the cellular chlorophyll content during transition into iron limitation. During recovery from iron limitation, chlorophyll is released from the complex and used for the reconstruction of photosystems. Therefore, the IsiA pigment-protein complex can play a critical role not only when cells transition into iron limitation, but also in supporting efficient recovery of the photosynthetic apparatus in the transition back out of the iron-limited state.

Three-dimensional ultrastructure and hyperspectral imaging of metabolite accumulation and dynamics in Haematococcus and Chlorella

Phycology has developed alongside light and electron microscopy techniques. Since the 1950s, progress in the field has accelerated dramatically with the advent of electron microscopy. Transmission electron microscopes can only acquire imaging data on a 2D plane. Currently, many of the life sciences are seeking to obtain 3D images with electron microscopy for the accurate interpretation of subcellular dynamics. Three-dimensional reconstruction using serial sections is a method that can cover relatively large cells or tissues without requiring special equipment. Another challenge is monitoring secondary metabolites (such as lipids or carotenoids) in intact cells. This became feasible with hyperspectral cameras, which enable the acquisition of wide-range spectral information in living cells. Here, we review bioimaging studies on the intracellular dynamics of substances such as lipids, carotenoids and phosphorus using conventional to state-of-the-art microscopy techniques in the field of algal biorefining.

Pigment-protein complexes are organized into stable microdomains in cyanobacterial thylakoids

Thylakoids are the place of the light-photosynthetic reactions. To gain maximal efficiency, these reactions are conditional to proper pigment-pigment and protein-protein interactions. In higher plants thylakoids, the interactions lead to a lateral asymmetry in localization of protein complexes (i.e. granal/stromal thylakoids) that have been defined as a domain-like structures characteristic by different biochemical composition and function (Albertsson P-Å. 2001,Trends Plant Science 6: 349-354). We explored this complex organization of thylakoid pigment-proteins at single cell level in the cyanobacterium Synechocystis sp. PCC 6803. Our 3D confocal images captured heterogeneous distribution of all main photosynthetic pigment-protein complexes (PPCs), Photosystem I (fluorescently tagged by YFP), Photosystem II and Phycobilisomes. The acquired images depicted cyanobacterial thylakoid membrane as a stable, mosaic-like structure formed by microdomains (MDs). These microcompartments are of sub-micrometer in sizes (~0.5-1.5 μm), typical by particular PPCs ratios and importantly without full segregation of observed complexes. The most prevailing MD is represented by MD with high Photosystem I content which allows also partial separation of Photosystems like in higher plants thylakoids. We assume that MDs stability (in minutes) provides optimal conditions for efficient excitation/electron transfer. The cyanobacterial MDs thus define thylakoid membrane organization as a system controlled by co-localization of three main PPCs leading to formation of thylakoid membrane mosaic. This organization might represent evolutional and functional precursor for the granal/stromal spatial heterogeneity in photosystems that is typical for higher plant thylakoids.

Protein arrangement factor: a new photosynthetic parameter characterizing the organization of thylakoid membrane proteins

A proper spatial distribution of photosynthetic pigment-protein complexes - PPCs (photosystems, light-harvesting antennas) is crucial for photosynthesis. In plants, photosystems I and II (PSI and PSII) are heterogeneously distributed between granal and stromal thylakoids. Here we have described similar heterogeneity in the PSI, PSII and phycobilisomes (PBSs) distribution in cyanobacteria thylakoids into microdomains by applying a new image processing method suitable for the Synechocystis sp. PCC6803 strain with yellow fluorescent protein-tagged PSI. The new image processing method is able to analyze the fluorescence ratios of PPCs on a single-cell level, pixel per pixel. Each cell pixel is plotted in CIE1931 color space by forming a pixel-color distribution of the cell. The most common position in CIE1931 is then defined as protein arrangement (PA) factor with xy coordinates. The PA-factor represents the most abundant fluorescence ratio of PSI/PSII/PBS, the 'mode color' of studied cell. We proved that a shift of the PA-factor from the center of the cell-pixel distribution (the 'median' cell color) is an indicator of the presence of special subcellular microdomain(s) with a unique PSI/PSII/PBS fluorescence ratio in comparison to other parts of the cell. Furthermore, during a 6-h high-light (HL) treatment, 'median' and 'mode' color (PA-factor) of the cell changed similarly on the population level, indicating that such microdomains with unique PSI/PSII/PBS fluorescence were not formed during HL (i.e. fluorescence changed equally in the whole cell). However, the PA-factor was very sensitive in characterizing the fluorescence ratios of PSI/PSII/PBS in cyanobacterial cells during HL by depicting a 4-phase acclimation to HL, and their physiological interpretation has been discussed.

Enhancement of photosynthesis in Synechococcus bacillaris by sponge-derived Ageladine A

This study is a proof of concept that the sponge derived pyrrole-imidazole alkaloid Ageladine A acts as an additional light harvesting molecule for photosynthesis of symbionts of marine sponges. The absorbance of Ageladine A is in the UV range and fluoresces blue, matching the blue absorbance of chlorophyll a. A joint modeling and experimental approach demonstrates that Ageladine A increases photosynthetic O₂ production of Synechococcus bacillaris WH5701 (CCMP1333), when the cells are exposed to UV light, which is marginally used for photosynthesis. Due to the presence of Ageladine A, production of O₂ increased 2.54 and 3.1-fold, in the experiments and the model, respectively.

Microscopy and Cell Biology: New Methods and New Questions

Understanding the cellular basis of human health and disease requires the spatial resolution of microscopy and the molecular-level details provided by spectroscopy. This review highlights imaging methods at the intersection of microscopy and spectroscopy with applications in cell biology. Imaging methods are divided into three broad categories: fluorescence microscopy, label-free approaches, and imaging tools that can be applied to multiple imaging modalities. Just as these imaging methods allow researchers to address new biological questions, progress in biological sciences will drive the development of new imaging methods. We highlight four topics in cell biology that illustrate the need for new imaging tools: nanoparticle-cell interactions, intracellular redox chemistry, neuroscience, and the increasing use of spheroids and organoids. Overall, our goal is to provide a brief overview of individual imaging methods and highlight recent advances in the use of microscopy for cell biology.

Spectral microscopic imaging of heterocysts and vegetative cells in two filamentous cyanobacteria based on spontaneous Raman scattering and photoluminescence by 976 nm excitation

Photosynthetic pigment-protein complexes are highly concentrated in thylakoid membranes of chloroplasts and cyanobacteria that emit strong autofluorescence (mainly 600-800 nm). In Raman scattering microscopy that enables imaging of pigment concentrations of thylakoid membranes, near infrared laser excitation at 1064 nm or visible laser excitation at 488-532 nm has been often employed in order to avoid the autofluorescence. Here we explored a new approach to Raman imaging of thylakoid membranes by using excitation wavelength of 976 nm. Two types of differentiated cells, heterocysts and vegetative cells, in two diazotrophic filamentous cyanobacteria, Anabaena variabilis, and Rivularia M-261, were characterized. Relative Raman scattering intensities of phycobilisomes of the heterocyst in comparison with the nearest vegetative cells of Rivularia remained at a significantly higher level than those of A. variabilis. It was also found that the 976 nm excitation induces photoluminescence around 1017-1175 nm from the two cyanobacteria, green alga (Parachlorella kessleri) and plant (Arabidopsis thaliana). We propose that this photoluminescence can be used as an index of concentration of chlorophyll a that has relatively small Raman scattering cross-sections. The Rivularia heterocysts that we analyzed were clearly classified into at least two subgroups based on the Chla-associated photoluminescence and carotenoid Raman bands, indicating two physiologically distinct states in the development or aging of the terminal heterocyst.

Carotenoid dynamics and lipid droplet containing astaxanthin in response to light in the green alga Haematococcus pluvialis

The unicellular green alga Haematococcus pluvialis accumulates large amounts of the red ketocarotenoid astaxanthin to protect against environmental stresses. Haematococcus cells that accumulate astaxanthin in the central part (green-red cyst cells) respond rapidly to intense light by distributing astaxanthin diffusively to the peripheral part of the cell within 10 min after irradiation. This response is reversible: when astaxanthin-diffused cells were placed in the dark, astaxanthin was redistributed to the center of the cell. Although Haematococcus possesses several pigments other that astaxanthin, the subcellular distribution and content of each pigment remain unknown. Here, we analyzed the subcellular dynamics and localization of major pigments such as astaxanthin, β-carotene, lutein, and chlorophylls under light irradiation using time-lapse and label-free hyperspectral imaging analysis. Fluorescence microscopy and freeze-fracture transmission electron microscopy showed that, preceding/following exposure to light, astaxanthin colocalized with lipid droplets, which moved from the center to the periphery through pathways in a chloroplast. This study revealed that photoresponse dynamics differed between astaxanthin and other pigments (chlorophylls, lutein, and β-carotene), and that only astaxanthin freely migrates from the center to the periphery of the cell through a large, spherical, cytoplasm-encapsulating chloroplast as a lipid droplet. We consider this to be the Haematococcus light-protection mechanism.

Dynamical localization of a thylakoid membrane binding protein is required for acquisition of photosynthetic competency

Vipp1 is highly conserved and essential for photosynthesis, but its function is unclear as it does not participate directly in light-dependent reactions. We analyzed Vipp1 localization in live cyanobacterial cells and show that Vipp1 is highly dynamic, continuously exchanging between a diffuse fraction that is uniformly distributed throughout the cell and a punctate fraction that is concentrated at high curvature regions of the thylakoid located at the cell periphery. Experimentally perturbing the spatial distribution of Vipp1 by relocalizing it to the nucleoid causes a severe growth defect during the transition from non-photosynthetic (dark) to photosynthetic (light) growth. However, the same perturbation of Vipp1 in dark alone or light alone growth conditions causes no growth or thylakoid morphology defects. We propose that the punctuated dynamics of Vipp1 at the cell periphery in regions of high thylakoid curvature enable acquisition of photosynthetic competency, perhaps by facilitating biogenesis of photosynthetic complexes involved in light-dependent reactions of photosynthesis.

Adjustments to Photosystem Stoichiometry and Electron Transfer Proteins Are Key to the Remarkably Fast Growth of the Cyanobacterium Synechococcus elongatus UTEX 2973

At the genome level, Synechococcus elongatus UTEX 2973 (Synechococcus 2973) is nearly identical to the model cyanobacterium Synechococcus elongatus PCC 7942 (Synechococcus 7942) with only 55 single nucleotide differences separating the two strains. Despite the high similarity between the two strains, Synechococcus 2973 grows three times faster, accumulates significantly more glycogen, is tolerant to extremely high light intensities, and displays higher photosynthetic rates. The high homology between the two strains provides a unique opportunity to examine the factors that lead to increased photosynthetic rates. We compared the photophysiology of the two strains and determined the differences in Synechococcus 2973 that lead to increased photosynthetic rates and the concomitant increase in biomass production. In this study, we identified inefficiencies in the electron transport chain of Synechococcus 7942 that have been alleviated in Synechococcus 2973. Photosystem II (PSII) capacity is the same in both strains. However, Synechococcus 2973 exhibits a 1.6-fold increase in PSI content, a 1.5-fold increase in cytochrome b₆f content, and a 2.4-fold increase in plastocyanin content on a per cell basis. The increased content of electron carriers allows a higher flux of electrons through the photosynthetic electron transport chain, while the increased PSI content provides more oxidizing power to maintain upstream carriers ready to accept electrons. These changes serve to increase the photosynthetic efficiency of Synechococcus 2973, the fastest growing cyanobacterium known.IMPORTANCE As the global population increases, the amount of arable land continues to decrease. To prevent a looming food crisis, crop productivity per acre must increase. A promising target for improving crop productivity is increasing the photosynthetic rates in crop plants. Cyanobacteria serve as models for higher plant photosynthetic systems and are an important test bed for improvements in photosynthetic productivity. In this study, we identified key factors that lead to improved photosynthetic efficiency and increased production of biomass of a cyanobacterium. We suggest that the findings presented herein will give direction to improvements that may be made in other photosynthetic organisms to improve photosynthetic efficiency.

Single-Cell Analysis Using Hyperspectral Imaging Modalities

Almost a decade ago, hyperspectral imaging (HSI) was employed by the NASA in satellite imaging applications such as remote sensing technology. This technology has since been extensively used in the exploration of minerals, agricultural purposes, water resources, and urban development needs. Due to recent advancements in optical re-construction and imaging, HSI can now be applied down to micro- and nanometer scales possibly allowing for exquisite control and analysis of single cell to complex biological systems. This short review provides a description of the working principle of the HSI technology and how HSI can be used to assist, substitute, and validate traditional imaging technologies. This is followed by a description of the use of HSI for biological analysis and medical diagnostics with emphasis on single-cell analysis using HSI.

Dissecting the Native Architecture and Dynamics of Cyanobacterial Photosynthetic Machinery

The structural dynamics and flexibility of cell membranes play fundamental roles in the functions of the cells, i.e., signaling, energy transduction, and physiological adaptation. The cyanobacterial thylakoid membrane represents a model membrane that can conduct both oxygenic photosynthesis and respiration simultaneously. In this study, we conducted direct visualization of the global organization and mobility of photosynthetic complexes in thylakoid membranes from a model cyanobacterium, Synechococcus elongatus PCC 7942, using high-resolution atomic force, confocal, and total internal reflection fluorescence microscopy. We visualized the native arrangement and dense packing of photosystem I (PSI), photosystem II (PSII), and cytochrome (Cyt) b₆f within thylakoid membranes at the molecular level. Furthermore, we functionally tagged PSI, PSII, Cyt b₆f, and ATP synthase individually with fluorescent proteins, and revealed the heterogeneous distribution of these four photosynthetic complexes and determined their dynamic features within the crowding membrane environment using live-cell fluorescence imaging. We characterized red light-induced clustering localization and adjustable diffusion of photosynthetic complexes in thylakoid membranes, representative of the reorganization of photosynthetic apparatus in response to environmental changes. Understanding the organization and dynamics of photosynthetic membranes is essential for rational design and construction of artificial photosynthetic systems to underpin bioenergy development. Knowledge of cyanobacterial thylakoid membranes could also be extended to other cell membranes, such as chloroplast and mitochondrial membranes.

Subcellular pigment distribution is altered under far-red light acclimation in cyanobacteria that contain chlorophyll f

Far-Red Light (FRL) acclimation is a process that has been observed in cyanobacteria and algae that can grow solely on light above 700 nm. The acclimation to FRL results in rearrangement and synthesis of new pigments and pigment-protein complexes. In this study, cyanobacteria containing chlorophyll f, Synechococcus sp. PCC 7335 and Halomicronema hongdechloris, were imaged as live cells with confocal microscopy. H. hongdechloris was further studied with hyperspectral confocal fluorescence microscopy (HCFM) and freeze-substituted thin-section transmission electron microscopy (TEM). Under FRL, phycocyanin-containing complexes and chlorophyll-containing complexes were determined to be physically separated and the synthesis of red-form phycobilisome and Chl f was increased. The timing of these responses was observed. The heterogeneity and eco-physiological response of the cells was noted. Additionally, a gliding motility for H. hongdechloris is reported.

Population-level coordination of pigment response in individual cyanobacterial cells under altered nitrogen levels

Cyanobacterial phycobilisome (PBS) pigment-protein complexes harvest light and transfer the energy to reaction centers. Previous ensemble studies have shown that cyanobacteria respond to changes in nutrient availability by modifying the structure of PBS complexes, but this process has not been visualized for individual pigments at the single-cell level due to spectral overlap. We characterized the response of four key photosynthetic pigments to nitrogen depletion and repletion at the subcellular level in individual, live Synechocystis sp. PCC 6803 cells using hyperspectral confocal fluorescence microscopy and multivariate image analysis. Our results revealed that PBS degradation and re-synthesis comprise a rapid response to nitrogen fluctuations, with coordinated populations of cells undergoing pigment modifications. Chlorophyll fluorescence originating from photosystem I and II decreased during nitrogen starvation, but no alteration in subcellular chlorophyll localization was found. We observed differential rod and core pigment responses to nitrogen deprivation, suggesting that PBS complexes undergo a stepwise degradation process.

High spatio-temporal-resolution detection of chlorophyll fluorescence dynamics from a single chloroplast with confocal imaging fluorometer

BACKGROUND

Chlorophyll fluorescence (CF) is a key indicator to study plant physiology or photosynthesis efficiency. Conventionally, CF is characterized by fluorometers, which only allows ensemble measurement through wide-field detection. For imaging fluorometers, the typical spatial and temporal resolutions are on the order of millimeter and second, far from enough to study cellular/sub-cellular CF dynamics. In addition, due to the lack of optical sectioning capability, conventional imaging fluorometers cannot identify CF from a single cell or even a single chloroplast.

RESULTS AND DISCUSSION

Here we demonstrated a fluorometer based on confocal imaging, that not only provides high contrast images, but also allows CF measurement with spatiotemporal resolution as high as micrometer and millisecond. CF transient (the Kautsky curve) from a single chloroplast is successfully obtained, with both the temporal dynamics and the intensity dependences corresponding well to the ensemble measurement from conventional studies. The significance of confocal imaging fluorometer is to identify the variation among individual chloroplasts, e.g. the temporal position of the P-S-M phases, and the half-life period of P-T decay in the Kautsky curve, that are not possible to analyze with wide-field techniques. A linear relationship is found between excitation intensity and the temporal positions of P-S-M peaks/valleys in the Kautsky curve. Based on the CF transients, the photosynthetic quantum efficiency is derived with spatial resolution down to a single chloroplast. In addition, an interesting 6-order increase in excitation intensity is found between wide-field and confocal fluorometers, whose pixel integration time and optical sectioning may account for this substantial difference.

CONCLUSION

Confocal imaging fluorometers provide micrometer and millisecond CF characterization, opening up unprecedented possibilities toward detailed spatiotemporal analysis of CF transients and its propagation dynamics, as well as photosynthesis efficiency analysis, on the scale of organelles, in a living plant.

Lateral Segregation of Photosystem I in Cyanobacterial Thylakoids

Photosystem I (PSI) is the dominant photosystem in cyanobacteria and it plays a pivotal role in cyanobacterial metabolism. Despite its biological importance, the native organization of PSI in cyanobacterial thylakoid membranes is poorly understood. Here, we use atomic force microscopy (AFM) to show that ordered, extensive macromolecular arrays of PSI complexes are present in thylakoids from Thermosynechococcus elongatus, Synechococcus sp PCC 7002, and Synechocystis sp PCC 6803. Hyperspectral confocal fluorescence microscopy and three-dimensional structured illumination microscopy of Synechocystis sp PCC 6803 cells visualize PSI domains within the context of the complete thylakoid system. Crystallographic and AFM data were used to build a structural model of a membrane landscape comprising 96 PSI trimers and 27,648 chlorophyll a molecules. Rather than facilitating intertrimer energy transfer, the close associations between PSI primarily maximize packing efficiency; short-range interactions with Complex I and cytochrome b6f are excluded from these regions of the membrane, so PSI turnover is sustained by long-distance diffusion of the electron donors at the membrane surface. Elsewhere, PSI-photosystem II contact zones provide sites for docking phycobilisomes and the formation of megacomplexes. PSI-enriched domains in cyanobacteria might foreshadow the partitioning of PSI into stromal lamellae in plants, similarly sustained by long-distance diffusion of electron carriers.

Lenslet array tunable snapshot imaging spectrometer (LATIS) for hyperspectral fluorescence microscopy

Snapshot hyperspectral imaging augments pixel dwell time and acquisition speeds over existing scanning systems, making it a powerful tool for fluorescence microscopy. While most snapshot systems contain fixed datacube parameters (x,y,λ), our novel snapshot system, called the lenslet array tunable snapshot imaging spectrometer (LATIS), demonstrates tuning its average spectral resolution from 22.66 nm (80x80x22) to 13.94 nm (88x88x46) over 485 to 660 nm. We also describe a fixed LATIS with a datacube of 200x200x27 for larger field-of-view (FOV) imaging. We report <1 sec exposure times and high resolution fluorescence imaging with minimal artifacts.

Hyperspectral fluorescence microscopy detects autofluorescent factors that can be exploited as a diagnostic method for Candida species differentiation

Fungi in the Candida genus are the most common fungal pathogens. They not only cause high morbidity and mortality but can also cost billions of dollars in healthcare. To alleviate this burden, early and accurate identification of Candida species is necessary. However, standard identification procedures can take days and have a large false negative error. The method described in this study takes advantage of hyperspectral confocal fluorescence microscopy, which enables the capability to quickly and accurately identify and characterize the unique autofluorescence spectra from different Candida species with up to 84% accuracy when grown in conditions that closely mimic physiological conditions.

Can spectral-spatial image segmentation be used to discriminate experimental burn wounds?

Hyperspectral imaging (HSI) is a noncontact and noninvasive optical modality emerging the field of medical research. The goal of this study was to determine the ability of HSI and image segmentation to discriminate burn wounds in a preclinical porcine model. A heated brass rod was used to introduce burn wounds of graded severity in a pig model and a sequence of hyperspectral data was recorded up to 8-h postinjury. The hyperspectral images were processed by an unsupervised spectral–spatial segmentation algorithm. Segmentation was validated using results from histology. The proposed algorithm was compared to K-means segmentation and was found superior. The obtained segmentation maps revealed separated zones within the burn sites, indicating a variation in burn severity. The suggested image-processing scheme allowed mapping dynamic changes of spectral properties within the burn wounds over time. The results of this study indicate that unsupervised spectral–spatial segmentation applied on hyperspectral images can discriminate burn injuries of varying severity.

Amphiphilic block copolymers as flexible membrane materials generating structural and functional mimics of green bacterial antenna complexes

We describe the ability of a short-chain amphiphilic block copolymer to self-assemble to form an artificial supramolecular light-harvesting system. Specifically, we demonstrate that the 2.5 kDa, poly(ethylene oxide)-block-poly(butadiene) (PEO-b-PBD), exhibits sufficient morphological flexibility as a membrane material and enables generation of mimics of three-dimensional chlorosomes as well as supported membrane bilayers containing energy acceptors. This overall architecture replicates green bacterial light-harvesting function whereby these assemblies exhibit long-range order and three-dimensional morphology similar to native chlorosomes and are capable of energy transfer internally and to external acceptors, located in a supporting biomimetic polymer membrane. Unlike native green bacterial systems that use multiple lipids as a matrix to generate the appropriate environment for chlorosome assembly and function, the described system matrix is comprised entirely of a single polymer amphiphile. This work demonstrates the potential of short-chain amphiphilic block copolymers in generating self-assembled, bio-mimetic membrane architectures, and in doing so, generates scalable, spatial-energetic landscapes for photonic applications. Finally, the results presented provide evidence of minimal requirements to induce chlorosome-like organization and function.

A complex carotenoid palette tunes avian colour vision

The brilliantly coloured cone oil droplets of the avian retina function as long-pass cut-off filters that tune the spectral sensitivity of the photoreceptors and are hypothesized to enhance colour discrimination and improve colour constancy. Although it has long been known that these droplets are pigmented with carotenoids, their precise composition has remained uncertain owing to the technical challenges of measuring these very small, dense and highly refractile optical organelles. In this study, we integrated results from high-performance liquid chromatography, hyperspectral microscopy and microspectrophotometry to obtain a comprehensive understanding of oil droplet carotenoid pigmentation in the chicken (Gallus gallus). We find that each of the four carotenoid-containing droplet types consists of a complex mixture of carotenoids, with a single predominant carotenoid determining the wavelength of the spectral filtering cut-off. Consistent with previous reports, we find that the predominant carotenoid type in the oil droplets of long-wavelength-sensitive, medium-wavelength-sensitive and short-wavelength-sensitive type 2 cones are astaxanthin, zeaxanthin and galloxanthin, respectively. In addition, the oil droplet of the principal member of the double cone contains a mixture of galloxanthin and two hydroxycarotenoids (lutein and zeaxanthin). Short-wavelength-absorbing apocarotenoids are present in all of the droplet types, providing filtering of light in a region of the spectrum where filtering by hydroxy- and ketocarotenoids may be incomplete. Thus, birds rely on a complex palette of carotenoid pigments within their cone oil droplets to achieve finely tuned spectral filtering.

A Novel Redoxin in the Thylakoid Membrane Regulates the Titer of Photosystem I

In photosynthetic organisms like cyanobacteria and plants, the main engines of oxygenic photosynthesis are the pigment-protein complexes photosystem I (PSI) and photosystem II (PSII) located in the thylakoid membrane. In the cyanobacterium Synechocystis sp. PCC 6803, the slr1796 gene encodes a single cysteine thioredoxin-like protein, orthologs of which are found in multiple cyanobacterial strains as well as chloroplasts of higher plants. Targeted inactivation of slr1796 in Synechocystis 6803 resulted in compromised photoautotrophic growth. The mutant displayed decreased chlorophyll a content. These changes correlated with a decrease in the PSI titer of the mutant cells, whereas the PSII content was unaffected. In the mutant, the transcript levels of genes for PSI structural and accessory proteins remained unaffected, whereas the levels of PSI structural proteins were severely diminished, indicating that Slr1796 acts at a posttranscriptional level. Biochemical analysis indicated that Slr1796 is an integral thylakoid membrane protein. We conclude that Slr1796 is a novel regulatory factor that modulates PSI titer.

Hyperspectral imaging of snow algae and green algae from aeroterrestrial habitats

Snow algae and green algae living in aeroterrestrial habitats are ideal objects to study adaptation to high light irradiation. Here, we used a detailed description of the spectral properties as a proxy for photo-acclimation/protection in snow algae (Chlamydomonas nivalis, Chlainomonas sp. and Chloromonas sp.) and charophyte green algae (Zygnema sp., Zygogonium ericetorum and Klebsormidium crenulatum). The hyperspectral microscopic mapping and imaging technique allowed us to acquire total absorption spectra of these microalgae in the waveband of 400-900nm. Particularly in Chlamydomonas nivalis and Chlainomonas sp., a high absorbance between 400-550nm was observed, due to naturally occurring secondary carotenoids; in Chloromonas sp. and in the charopyhte algae this high absorbance was missing, the latter being close relatives to land plants. To investigate if cellular water loss has an influence on the spectral properties, the cells were plasmolysed in sorbitol or desiccated at ambient air. While in snow algae, these treatments did hardly change the spectral properties, in the charopyhte algae the condensation of the cytoplasm and plastids increased the absorbance in the lower waveband of 400-500nm. These changes might be ecologically relevant and photoprotective, as aeroterrestrial algae are naturally exposed to occasional water limitation, leading to desiccation, which are conditions usually occurring together with higher irradiation.