Dynamic NanoSIMS ion imaging of unicellular freshwater algae exposed to copper

Introducing FISCAS, a Tool for the Effective Generation of Single Cell MALDI-MSI Data

We introduce Fluorescence Integrated Single-Cell Analysis Script (FISCAS), which combines fluorescence microscopy with MALDI-MSI to streamline single-cell analysis. FISCAS enables automated selection of tight measurement regions, thereby reducing the acquisition of off-target pixels, and makes use of established algorithms for cell segmentation and coregistration to rapidly compile single-cell spectra. MALDI-compatible staining of membranes, nuclei, and lipid droplets allows the collection of fluorescence data prior to the MALDI-MSI measurement on a timsTOF fleX MALDI-2. Usefulness of the software is demonstrated by the example of THP-1 cells during stimulated differentiation into macrophages at different time points. In this proof-of-principle study, FISCAS was used to automatically generate single-cell mass spectra along with a wide range of morphometric parameters for a total number of roughly 1300 cells collected at 24, 48, and 72 h after the onset of stimulation. Data analysis of the combined morphometric and single-cell mass spectrometry data shows significant molecular heterogeneity within the cell population at each time point, indicating an independent differentiation of each individual cell rather than a synchronized mechanism. Here, the grouping of cells based on their molecular phenotype revealed an overall clearer distinction of the different phases of differentiation into macrophages and delivered an increased number of lipid signals as possible markers compared with traditional bulk analysis. Utilizing the linkage between mass spectrometric data and fluorescence microscopy confirmed the expected positive correlation between lipid droplet staining and the overall signal for triacylglyceride (TG), demonstrating the usefulness of this multimodal approach.

Ultrahigh-resolution imaging of biogenic phosphorus and molybdenum in palaeoproterozoic gunflint microfossils

Phosphorus and molybdenum play important roles in the formation of microbial cell structures and specific enzymes crucial for metabolic processes. Nevertheless, questions remain about the preservation of these elements within ancient microfossils. Here, we present shape-accurate ion images capturing phosphorus and molybdenum on Palaeoproterozoic filamentous microfossils by pioneering a methodology using lateral high-resolution secondary ion mass spectrometry. Introducing electrically conductive glass for mounting isolated microfossils facilitated clearer observations with increased secondary ion yields. Phosphorus was detected along the contours of microfossils, providing direct evidence of phospholipid utilization in the cell membrane. Trace amounts of molybdenum were detected within microfossil bodies, suggesting potential remnants of molybdenum-bearing proteins, such as nitrogenase. These findings align with the hypothesized cyanobacterial origin of filamentous gunflint microfossils. Our methodology introduces a groundbreaking tool for obtaining crucial insights into the cellular evolution and metabolic pathways of microorganisms, allowing comparisons of their morphological characteristics.

Recent advances in mass spectrometry imaging of single cells

Mass spectrometry imaging (MSI) is a sensitive, specific, label-free imaging analysis technique that can simultaneously obtain the spatial distribution, relative content, and structural information of hundreds of biomolecules in cells and tissues, such as lipids, small drug molecules, peptides, proteins, and other compounds. The study of molecular mapping of single cells can reveal major scientific issues such as the activity pattern of living organisms, disease pathogenesis, drug-targeted therapy, and cellular heterogeneity. Applying MSI technology to the molecular mapping of single cells can provide new insights and ideas for the study of single-cell metabolomics. This review aims to provide an informative resource for those in the MSI community who are interested in single-cell imaging. Particularly, we discuss advances in imaging schemes and sample preparation, instrumentation improvements, data processing and analysis, and 3D MSI over the past few years that have allowed MSI to emerge as a powerful technique in the molecular imaging of single cells. Also, we highlight some of the most cutting-edge studies in single-cell MSI, demonstrating the future potential of single-cell MSI. Visualizing molecular distribution at the single-cell or even sub-cellular level can provide us with richer cell information, which strongly contributes to advancing research fields such as biomedicine, life sciences, pharmacodynamic testing, and metabolomics. At the end of the review, we summarize the current development of single-cell MSI technology and look into the future of this technology.

Imaging biofilms using fluorescence in situ hybridization: seeing is believing

Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.

Science Autonomy for Ocean Worlds Astrobiology: A Perspective

Astrobiology missions to ocean worlds in our solar system must overcome both scientific and technological challenges due to extreme temperature and radiation conditions, long communication times, and limited bandwidth. While such tools could not replace ground-based analysis by science and engineering teams, machine learning algorithms could enhance the science return of these missions through development of autonomous science capabilities. Examples of science autonomy include onboard data analysis and subsequent instrument optimization, data prioritization (for transmission), and real-time decision-making based on data analysis. Similar advances could be made to develop streamlined data processing software for rapid ground-based analyses. Here we discuss several ways machine learning and autonomy could be used for astrobiology missions, including landing site selection, prioritization and targeting of samples, classification of "features" (e.g., proposed biosignatures) and novelties (uncharacterized, "new" features, which may be of most interest to agnostic astrobiological investigations), and data transmission.

Intracellular Biotransformation of Cu(II)/Cu(I) Explained High Cu Toxicity to Phytoplankton Chlamydomonas reinhardtii

The toxicity of Cu is related to its redox species, but the differential toxicity of Cu(II) and Cu(I) remains unknown. In the present study, we developed a novel protocol to simultaneously detect the biologically produced extracellular Cu(I) and internalized Cu(II) in a freshwater phytoplankton Chlamydomonas reinhardtii. The intracellular Cu(I) was further imaged using a fluorometric probe. Combining these pieces of evidence, we demonstrated that Cu(I) dominated the Cu toxicity in algal cells under Fe-deficient conditions. Our results showed that the labile Cu(I) content increased significantly in the low Fe quota cells. Intracellular biotransformation from Cu(II) to Cu(I) rather than the direct uptake of Cu(I) was responsible for the high Cu toxicity. The abnormal biotransformation from Cu(II) to Cu(I) under Fe deficiency was not resulted from the increase of overall Cu bioaccumulation but was likely due to the change of Cu(II) metabolism. High contents of Cu(II) were accumulated in the normal cells and the low Zn quota cells upon Cu exposure but did not induce cell death, further suggesting that Cu(I) dominated the Cu toxicity to the algae. This is the first study to simultaneously consider the effect of Cu(I) and Cu(II) during Cu exposure in phytoplankton. The results uncovered the underlying mechanisms of high Cu toxicity under Fe deficiency and highlighted the critical role of modulation of Cu metabolism in phytoplankton.

FISH Variants

FISH has gained an irreplaceable place in microbiology because of its ability to detect and locate a microorganism, or a group of organisms, within complex samples. However, FISH role has evolved drastically in the last few decades and its value has been boosted by several advances in signal intensity, imaging acquisitions, automation, method robustness, and, thus, versatility. This has resulted in a range of FISH variants that gave researchers the ability to access a variety of other valuable information such as complex population composition, metabolic activity, gene detection/quantification, or subcellular location of genetic elements. In this chapter, we will review the more relevant FISH variants, their intended use, and how they address particular challenges of classical FISH.

Across the spectrum: integrating multidimensional metal analytics for in situ metallomic imaging

To know how much of a metal species is in a particular location within a biological context at any given time is essential for understanding the intricate roles of metals in biology and is the fundamental question upon which the field of metallomics was born. Simply put, seeing is powerful. With the combination of spectroscopy and microscopy, we can now see metals within complex biological matrices complemented by information about associated molecules and their structures. With the addition of mass spectrometry and particle beam based techniques, the field of view grows to cover greater sensitivities and spatial resolutions, addressing structural, functional and quantitative metallomic questions from the atomic level to whole body processes. In this perspective, I present a paradigm shift in the way we relate to and integrate current and developing metallomic analytics, highlighting both familiar and perhaps less well-known state of the art techniques for in situ metallomic imaging, specific biological applications, and their use in correlative studies. There is a genuine need to abandon scientific silos and, through the establishment of a metallomic scientific platform for further development of multidimensional analytics for in situ metallomic imaging, we have an incredible opportunity to enhance the field of metallomics and demonstrate how discovery research can be done more effectively.

Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in manganese-deficient conditions

Exposing cells to excess metal concentrations well beyond the cellular quota is a powerful tool for understanding the molecular mechanisms of metal homeostasis. Such improved understanding may enable bioengineering of organisms with improved nutrition and bioremediation capacity. We report here that Chlamydomonas reinhardtii can accumulate manganese (Mn) in proportion to extracellular supply, up to 30-fold greater than its typical quota and with remarkable tolerance. As visualized by X-ray fluorescence microscopy and nanoscale secondary ion MS (nanoSIMS), Mn largely co-localizes with phosphorus (P) and calcium (Ca), consistent with the Mn-accumulating site being an acidic vacuole, known as the acidocalcisome. Vacuolar Mn stores are accessible reserves that can be mobilized in Mn-deficient conditions to support algal growth. We noted that Mn accumulation depends on cellular polyphosphate (polyP) content, indicated by 1) a consistent failure of C. reinhardtii vtc1 mutant strains, which are deficient in polyphosphate synthesis, to accumulate Mn and 2) a drastic reduction of the Mn storage capacity in P-deficient cells. Rather surprisingly, X-ray absorption spectroscopy, EPR, and electron nuclear double resonance revealed that only little Mn²⁺ is stably complexed with polyP, indicating that polyP is not the final Mn ligand. We propose that polyPs are a critical component of Mn accumulation in Chlamydomonas by driving Mn relocation from the cytosol to acidocalcisomes. Within these structures, polyP may, in turn, escort vacuolar Mn to a number of storage ligands, including phosphate and phytate, and other, yet unidentified, compounds.

Iron Modulation of Copper Uptake and Toxicity in a Green Alga ( Chlamydomonas reinhardtii)

Little attention has been paid to the role of essential trace elements on the toxicity of another element. In this work, we examined if low concentrations of essential elements (Co, Mn, Zn, and Fe) modified the response of a freshwater green alga ( Chlamydomonas reinhardtii) to copper. To do so, we followed cell growth over 72 h in exposure media where the essential element concentrations were manipulated. Among these elements, iron proved to have a strong impact on the cells' response to copper. The free Cu²⁺ concentrations required to inhibit cellular growth by 50% (EC50) over 72 h decreased from 2 nM in regular Fe medium (10^-17.6 M Fe³⁺) to 4 pM in low iron medium (10^-19.0 M Fe³⁺); a 500-fold increase in toxicity. Moreover, at low Cu²⁺ concentrations (10^-13.0 to 10^-10.5 M), Cu uptake increased under low iron conditions but remain relatively stable under regular iron conditions. These results show clearly that iron plays a protective role against copper uptake and toxicity to C. reinhardtii. In freshwaters, iron is always abundant but the expected free iron concentrations in surface waters can vary between 10^-14.0 to 10^-20.0 M, depending on pH (e.g., when pH increases from 6 to 8). We conclude that copper toxicity in natural waters can be modulated by iron and that, in some conditions, the Biotic Ligand Model may need to be further developed to account for the influence of iron.

Combined Effects of Trace Metals and Light on Photosynthetic Microorganisms in Aquatic Environment

In the present review, we critically examine the state-of-the-art of the research on combined effects of trace metals and light on photosynthetic microorganisms in aquatic environment. Light of different intensity and spectral composition affects the interactions between trace metals and photosynthetic microorganisms directly, by affecting vital cellular functions and metal toxicokinetics and toxicodynamics, and indirectly, by changing ambient medium characteristics. Light radiation and in particular, the ultraviolet radiation component (UVR) alters the structure and reactivity of dissolved organic matter in natural water, which in most of the cases decreases its metal binding capacity and enhances metal bioavailability. The increase of cellular metal concentrations is generally associated with increasing light intensity, however further studies are necessary to better understand the underlying mechanisms. Studies on the combined exposures of photosynthetic microorganisms to metals and UVR reveal antagonistic, additive or synergistic interactions depending on light intensity, spectral composition or light pre-exposure history. Among the light spectrum components, most of the research was performed with UVR, while the knowledge on the role of high-intensity visible light and environmentally relevant solar light radiation is still limited. The extent of combined effects also depends on the exposure sequence and duration, as well as the species-specific sensitivity of the tested microorganisms and the activation of stress defense responses.

New Frontiers of Metallomics: Elemental and Species-Specific Analysis and Imaging of Single Cells

Single cells represent the basic building units of life, and thus their study is one the most important areas of research. However, classical analysis of biological cells eludes the investigation of cell-to-cell differences to obtain information about the intracellular distribution since it only provides information by averaging over a huge number of cells. For this reason, chemical analysis of single cells is an expanding area of research nowadays. In this context, metallomics research is going down to the single-cell level, where high-resolution high-sensitive analytical techniques are required. In this chapter, we present the latest developments and applications in the fields of single-cell inductively coupled plasma mass spectrometry (SC-ICP-MS), mass cytometry, laser ablation (LA)-ICP-MS, nanoscale secondary ion mass spectrometry (nanoSIMS), and synchrotron X-ray fluorescence microscopy (SXRF) for single-cell analysis. Moreover, the capabilities and limitations of the current analytical techniques to unravel single-cell metabolomics as well as future perspectives in this field will be discussed.

In Situ Subcellular Imaging of Copper and Zinc in Contaminated Oysters Revealed by Nanoscale Secondary Ion Mass Spectrometry

Determining the in situ localization of trace elements at high lateral resolution levels in the biological system is very challenging, but critical for our understanding of metal sequestration and detoxification. Here, the cellular and subcellular distributions of Cu and Zn in contaminated oysters of Crassostrea hongkongensis were for the first time mapped using nanoscale secondary ion mass spectrometry (nanoSIMS). Three types of metal-containing cells were revealed in the gill and mantle of oysters, including Cu-specific hemocytes, Cu and Zn-containing granular hemocytes, and Cu and Zn-containing calcium cells. Obvious intercellular distribution of Cu was found in the gill tissue, indicating the potential role of hemolymph in the transportation of Cu in oysters. The distribution of Cu showed a strong colocalization with sulfur and nitrogen in Cu-specific hemocyte and intercellular hemolymph. In the Cu and Zn-containing granular hemocytes and calcium cells, the co-occurrence of Cu and Zn with phosphorus and calcium was also found. Different relationships of distributions between Cu/Zn and macronutrient elements (nitrogen, sulfur and phosphorus) implied the differential metal complexation in oysters. Interestingly, quantitative analysis of the ratios of ³²S^-/¹²C¹⁴N^- and ³¹P^-/¹²C¹⁴N^- of metal-deposited sites suggested the dynamic process of transfer of Cu and Zn from the metabolized protein pool to a more thermodynamically stable and detoxified form.

NanoSIMS for biological applications: Current practices and analyses

Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.

In situ monitoring of molecular changes during cell differentiation processes in marine macroalgae through mass spectrometric imaging

Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) was employed to discriminate between cell differentiation processes in macroalgae. One of the key developmental processes in the algal life cycle is the production of germ cells (gametes and zoids). The gametogenesis of the marine green macroalga Ulva mutabilis (Chlorophyta) was monitored by metabolomic snapshots of the surface, when blade cells differentiate synchronously into gametangia and giving rise to gametes. To establish MSI for macroalgae, dimethylsulfoniopropionate (DMSP), a known algal osmolyte, was determined. MSI of the surface of U. mutabilis followed by chemometric data analysis revealed dynamic metabolomic changes during cell differentiation. DMSP and a total of 55 specific molecular biomarkers, which could be assigned to important stages of the gametogenesis, were detected. Our research contributes to the understanding of molecular mechanisms underlying macroalgal cell differentiation. Graphical abstract Molecular changes during cell differentiation of the marine macroalga Ulva were visualized by matrix assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI).

Analysis of Chemotherapeutic Drug Delivery at the Single Cell Level Using 3D-MSI-TOF-SIMS

In this work, we show the advantages of label-free, tridimensional mass spectrometry imaging using dual beam analysis (25 keV Bi₃⁺) and depth profiling (20 keV with a distribution centered at Ar₁₅₀₀⁺) coupled to time of flight secondary ion mass spectrometry (3D-MSI-TOF-SIMS) for the study of A-172 human glioblastoma cell line treated with B-cell lymphoma 2 (Bcl-2) inhibitor ABT-737. The high spatial (~250 nm) and high mass resolution (m/Δm ~10,000) of TOF-SIMS permitted the localization and identification of the intact, unlabeled drug molecular ion (m/z 811.26 C₄₂H₄₄ClN₆O₅S₂^- [M - H]^-) as well as characteristic fragment ions. We propose a novel approach based on the inspection of the drug secondary ion yield, which showed a good correlation with the drug concentration during cell treatment at therapeutic dosages (0-200 μM with 4 h incubation). Chemical maps using endogenous molecular markers showed that the ABT-737 is mainly localized in subsurface regions and absent in the nucleus. A semiquantitative workflow is proposed to account for the biological cell diversity based on the spatial distribution of endogenous molecular markers (e.g., nuclei and cytoplasm) and secondary ion confirmation based on the ratio of drug-specific fragments to molecular ion as a function of the therapeutic dosage. Graphical Abstract ᅟ.

Chemical bioimaging for the subcellular localization of trace elements by high contrast TEM, TEM/X-EDS, and NanoSIMS

Chemical bioimaging offers an important contribution to the investigation of biochemical functions, biosorption and bioaccumulation processes of trace elements via their localization at the cellular and even at the subcellular level. This paper describes the combined use of high contrast transmission electron microscopy (HC-TEM), energy dispersive X-ray spectroscopy (X-EDS), and nano secondary ion mass spectrometry (NanoSIMS) applied to a model organism, the unicellular green algae Chlamydomonas reinhardtii. HC-TEM providing a lateral resolution of 1nm was used for imaging the ultrastructure of algae cells which have diameters of 5-10μm. TEM coupled to X-EDS (TEM/X-EDS) combined textural (morphology and size) analysis with detection of Ca, P, K, Mg, Fe, and Zn in selected subcellular granules using an X-EDS probe size of approx. 1μm. However, instrumental sensitivity was at the limit for trace element detection. NanoSIMS allowed chemical imaging of macro and trace elements with subcellular resolution (element mapping). Ca, Mg, and P as well as the trace elements Fe, Cu, and Zn present at basal levels were detected in pyrenoids, contractile vacuoles, and granules. Some metals were even localized in small vesicles of about 200nm size. Sensitive subcellular localization of trace metals was possible by the application of a recently developed RF plasma oxygen primary ion source on NanoSIMS which has shown good improvements in terms of lateral resolution (below 50nm), sensitivity, and stability. Furthermore correlative single cell imaging was developed combining the advantages of TEM and NanoSIMS. An advanced sample preparation protocol provided adjacent ultramicrotome sections for parallel TEM and NanoSIMS analyses of the same cell. Thus, the C. reinhardtii cellular ultrastructure could be directly related to the spatial distribution of metals in different cell organelles such as vacuoles and chloroplast.

Bridging the divide between human and environmental nanotoxicology

The need to assess the human and environmental risks of nanoscale materials has prompted the development of new metrological tools for their detection, quantification and characterization. Some of these methods have tremendous potential for use in various scenarios of nanotoxicology. However, in some cases, the limited dialogue between environmental scientists and human toxicologists has hampered the full exploitation of these resources. Here we review recent progress in the development of methods for nanomaterial analysis and discuss the use of these methods in environmental and human toxicology. We highlight the opportunities for collaboration between these two research areas.

Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas

We identified a Cu-accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulates Cu, a process dependent on the nutritional Cu sensor CRR1, but it is functionally Cu deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. Nano-secondary ion MS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy was consistent with Cu(+) accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu(+) became bioavailable for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mismetallation during Zn deficiency and enabling efficient cuproprotein metallation or remetallation upon Zn resupply.

Current status and future perspectives of mass spectrometry imaging

Mass spectrometry imaging is employed for mapping proteins, lipids and metabolites in biological tissues in a morphological context. Although initially developed as a tool for biomarker discovery by imaging the distribution of protein/peptide in tissue sections, the high sensitivity and molecular specificity of this technique have enabled its application to biomolecules, other than proteins, even in cells, latent finger prints and whole organisms. Relatively simple, with no requirement for labelling, homogenization, extraction or reconstitution, the technique has found a variety of applications in molecular biology, pathology, pharmacology and toxicology. By discriminating the spatial distribution of biomolecules in serial sections of tissues, biomarkers of lesions and the biological responses to stressors or diseases can be better understood in the context of structure and function. In this review, we have discussed the advances in the different aspects of mass spectrometry imaging processes, application towards different disciplines and relevance to the field of toxicology.

Interactions between diatoms and bacteria

Diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. Diatoms are responsible for one-fifth of the photosynthesis on Earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. Through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic levels. Here we present an overview of how diatoms and bacteria interact and the implications of these interactions. We emphasize that heterotrophic bacteria in the oceans that are consistently associated with diatoms are confined to two phyla. These consistent bacterial associations result from encounter mechanisms that occur within a microscale environment surrounding a diatom cell. We review signaling mechanisms that occur in this microenvironment to pave the way for specific interactions. Finally, we discuss known interactions between diatoms and bacteria and exciting new directions and research opportunities in this field. Throughout the review, we emphasize new technological advances that will help in the discovery of new interactions. Deciphering the languages of diatoms and bacteria and how they interact will inform our understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans.

Mass Spectrometry Imaging: facts and perspectives from a non-mass spectrometrist point of view

Mass Spectrometry Imaging (MSI, also called Imaging Mass Spectrometry) can be used to map molecules according to their chemical abundance and spatial distribution. This technique is not widely used in mass spectrometry circles and is barely known by other scientists. In this review, a brief overview of the mass spectrometer hardware used in MSI and some of the possible applications of this powerful technique are discussed. I intend to call attention to MSI uses from cell biology to histopathology for biological scientists who have little background in mass spectrometry. MSI facts and perspectives are presented from a non-mass spectrometrist point of view.

Compositional mapping of the surface and interior of mammalian cells at submicrometer resolution

We present progress toward imaging of chemical species within intact mammalian cells using secondary ion mass spectrometry, including the simultaneous mapping of subcellular elemental and molecular species along with intrinsic membrane-specific cellular markers. Results from imaging both the cell surface and cell interior exposed by site-specific focused ion beam milling demonstrate that in-plane resolutions of approximately 400-500 nm can be achieved. The results from mapping cell surface phosphatidylcholine and several other molecular ions present in the cells establish that spatially resolved chemical signatures of individual cells can be derived from novel multivariate analysis and classification of the molecular images obtained at different m/z ratios. The methods we present here for specimen preparation and chemical imaging of cell interiors provide the foundation for obtaining 3D molecular maps of unstained mammalian cells, with particular relevance for probing the subcellular distributions of small molecules, such as drugs and metabolites.

Identification of diazotrophic microorganisms in marine sediment via fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS)

Growing appreciation for the biogeochemical significance of uncultured microorganisms is changing the focus of environmental microbiology. Techniques designed to investigate microbial metabolism in situ are increasingly popular, from mRNA-targeted fluorescence in situ hybridization (FISH) to the "-omics" revolution, including metagenomics, transcriptomics, and proteomics. Recently, the coupling of FISH with nanometer-scale secondary ion mass spectrometry (NanoSIMS) has taken this movement in a new direction, allowing single-cell metabolic analysis of uncultured microbial phylogenic groups. The main advantage of FISH-NanoSIMS over previous noncultivation-based techniques to probe metabolism is its ability to directly link 16S rRNA phylogenetic identity to metabolic function. In the following chapter, we describe the procedures necessary to identify nitrogen-fixing microbes within marine sediment via FISH-NanoSIMS, using our work on nitrogen fixation by uncultured deep-sea methane-consuming archaea as a case study.

Recent Advances in Mapping the Sub-cellular Distribution of Metal-Based Anticancer Drugs

There are increasing reports of novel metal-based chemotherapeutics that have either improved cancer cell selectivity, or alternative mechanisms of action, to existing anticancer drugs, and techniques are required for determining their sub-cellular molecular targets. Imaging methods offer many distinct advantages over destructive fractionation techniques, including the preservation of useful morphological information; however, mapping the intracellular distribution of metal ions inside tumour cells still remains challenging. Recent advances in three modes of imaging are discussed in this review, with a particular focus on the application to metal-based cancer chemotherapy – fluorescence microscopy, electron microscopy (including energy-filtered transmission electron microscopy (EFTEM)), and a new technique, Nano-scale secondary ion mass spectrometry (NanoSIMS).

Matrix-assisted laser desorption/ionization imaging mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool that enables the simultaneous detection and identification of biomolecules in analytes. MALDI-imaging mass spectrometry (MALDI-IMS) is a two-dimensional MALDI-mass spectrometric technique used to visualize the spatial distribution of biomolecules without extraction, purification, separation, or labeling of biological samples. MALDI-IMS has revealed the characteristic distribution of several biomolecules, including proteins, peptides, amino acids, lipids, carbohydrates, and nucleotides, in various tissues. The versatility of MALDI-IMS has opened a new frontier in several fields such as medicine, agriculture, biology, pharmacology, and pathology. MALDI-IMS has a great potential for discovery of unknown biomarkers. In this review, we describe the methodology and applications of MALDI-IMS for biological samples.

High-resolution elemental localization in vacuolate plant cells by nanoscale secondary ion mass spectrometry

By combining the capabilities of advanced sample preparation methodologies with the latest generation of secondary ion mass spectrometry instrumentation, we show that chemical information on the distribution of even dilute species in biological samples can be obtained with spatial resolutions of better than 100 nm. Here, we show the distribution of nickel and other elements in leaf tissue of the nickel hyperaccumulator plant Alyssum lesbiacum prepared by high-pressure freezing and freeze substitution.

Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo-microbial processes

The application of secondary ion mass spectrometry (SIMS) has tremendous value for the field of geobiology, representing a powerful tool for identifying the specific role of micro-organisms in biogeochemical cycles. In this review, we highlight a number of diverse applications for SIMS and nanoSIMS in geobiological research. SIMS performs isotope and elemental analysis at microscale enabling the investigation of the physiology of individual microbes within complex communities. Additionally, through the study of isotopic or chemical characteristics that are common in both living and ancient microbial communities, SIMS allows for direct comparisons of potential biosignatures derived from extant microbial cells and their fossil equivalents.

Effect of humic acid on Cd(II), Cu(II), and Pb(II) uptake by freshwater algae: kinetic and cell wall speciation considerations

Thepresent study examines the effect of humic acid on the uptake kinetics of Cd(II), Cu(II), and Pb(II) by the freshwater alga Chlorella kesslerii. The results demonstrated that the relative proportion of Pb in the cell wall layer is greater than that of the internalized Pb, while internalized Cd and Cu were comparable or greater than the adsorbed metal concentration. In the presence of 10 mg L(-1) humic acid (HA), Cd and Cu uptake kinetics were consistent with that predicted by measured free metal concentrations. For Pb, the uptake flux and amount of lead bound to internalization and adsorption sites were an order of magnitude higher than those found at the same free lead ion concentrations in the presence of citric acid. Chemodynamic modeling suggested that the enhancement of the Pb uptake flux in the presence of HA originates from an increasing amount of Pb bound to the internalization sites through a ternary complex formation between lead-humic acid complex and internalization sites. Cell wall speciation calculations indicated that the lead-humic acid complex is the predominant species in the cell wall layer, while for Cu(II) and Cd(II) metal bound to the internalization (Cu) and adsorption (Cd) sites significantly dominated over the M-HA complex. The findings of the work show the relevance of the cell wall layer concentration and speciation and its key role in defining the local equilibrium conditions between metal and internalizations sites. The results of the present kinetic study have important consequences for improvement of the mechanistic understanding of the role of dissolved organic matter in metal uptake in phytoplankton and biogeochemical cycling of metals in the surface waters.