Comprehensive Bio-Imaging with Fluorinated Nanoparticles Using Breathable Liquids

Abstract

Fluorocarbons are lipophobic and non-polar molecules that exhibit remarkable bio-compatibility, with applications in liquid ventilation and synthetic blood. The unique properties of these compounds have also enabled mass spectrometry imaging of tissues where the fluorocarbons act as a Teflon-like coating for nanostructured surfaces to assist in desorption/ionization. Here we report fluorinated gold nanoparticles (f-AuNPs) designed to facilitate nanostructure imaging mass spectrometry. Irradiation of f-AuNPs results in the release of the fluorocarbon ligands providing a driving force for analyte desorption. The f-AuNPs allow for the mass spectrometry analysis of both lipophilic and polar (central carbon) metabolites. An important property of AuNPs is that they also act as contrast agents for X-ray microtomography and electron microscopy, a feature we have exploited by infusing f-AuNPs into tissue via fluorocarbon liquids to facilitate multi-modal (molecular and anatomical) imaging.

Introduction

Fluorocarbons have remarkable chemical and physical characteristics that allow unique surface properties, high stability, low reactivity, and an ability to solubilize gases. The bio-compatibility of fluorocarbons has been demonstrated ^1-5 and has inspired researchers to utilize these compounds for a wide range biomedical and research applications. For example these properties have enabled fluorocarbons to be applied in areas as diverse as surface coatings⁶, drug delivery⁴, liquid ventilation¹, synthetic blood² and several imaging modalities^4,5,7,8 including mass spectrometry imaging⁹.

Mass spectrometry imaging facilitates the spatially resolved mass analysis of metabolites in situ^10-12 where investigators have a choice of multiple technologies each with their inherent advantages and disadvantages^9,13-18. These techniques include matrix-assisted laser desorption/ionization mass spectrometry (MALDIMS)¹⁵, secondary ion mass spectrometry (SIMS)¹³, desorption electrospray ionization (DESI)¹⁴, MALDESI¹⁸, and others^9,16,17,19. While there have been some successful developments in low energy²⁰ and low background²¹ matrices for MALDI-MS, the most widely used of these technologies, these matrices do not facilitate multiple modes imaging.

Gold nanoparticles (AuNPs) are well known as contrast agents for X-ray imaging technologies^22-24 and electron microscopy²⁵. For example, the attenuation property of X-rays by AuNPs has led to their use as contrast agents in computed tomography (CT) imaging^26,27. AuNP have also been exploited for mass spectrometry molecular imaging, thus presenting a single platform capable of supporting comprehensive bio-imaging. However, AuNPs ability to facilitate molecular imaging via mass spectrometry is limited due to the required high laser energies, resulting in significant fragmentation and generally poor sensitivity²⁸. While AuNPs are attractive biomedical imaging agents, they have not been explored as agents to correlate structure with molecular information given their limitations with mass spectrometry. Indeed, when performing mass spectrometry-based metabolomic imaging, correlating metabolite localization patterns with tissue anatomy is key to data interpretation but has represented a serious challenge. Traditionally, correlations have been based on immunohistochemistry. Given that immunohistochemistry chemically alters tissue sections and therefore is incompatible with mass spectrometry imaging, however, the immunohistochemistry and mass spectrometry imaging cannot be performed on the same tissue samples.

Here we introduce f-AuNPs as an agent for nanostructure imaging mass spectrometry (NIMS). The use of fluorocarbons as a covalent modification of AuNPs for this application is a natural choice given the history¹⁷ of fluorocarbons facilitating NIMS, specifically nanostructured silicon has benefited from fluorine modifications⁹. Fluorinated silicon nanostructures used for laser desorption/ionization have been shown to generate low background interference, have minimal UV-absorbance, generate little fragmentation and, given their unique super-hydrophobicity, readily allow for the desorption of metabolites from their surface with high sensitivity. Additionally, fluorous initiators containing amino groups can be used to promote [M-H]^- production^29,30, which, similar to basic MALDI matrices^31,32 have been successfully applied to mass spectrometry imaging of central carbon metabolites. In addition to mass spectrometry imaging f-AuNPs, unlike MALDI matricies, are also capable of acting as contrast agents for X-ray analysis and electron microscopy^22-24,25. We demonstrate f-AuNP multi-modal imaging to generate X-ray (μCT) and electron microscopy structural images, as well as facilitating mass spectrometry imaging, providing both anatomical and molecular information.

Results

Fluorinated Gold Nanoparticles for mass spectrometry imaging

Given the advantages that fluorocarbon modifications impart on silicon nanostructure mass spectrometry imaging, our goal in these studies was to adapt fluorocarbon ligands to the more versatile gold nanoparticles. In laser desorption/ionization experiments, silicon nanostructures and gold nanoparticles absorb energy extremely well in the ultra violet region ^33-35 and in the case of AuNPs the core can reach ∼2000 K in a few nanoseconds³⁶. While AuNPs alone have limited ability to facilitate molecular imaging via mass spectrometry due to the required high laser energies resulting in significant fragmentation and generally poor sensitivity²⁸, AuNPs with fluorocarbon ligands added to the nanoparticle surface (f-AuNPs) are designed to initiate the desorption/ionization mass spectrometry event while attenuating energy transfer to the analyte. This is accomplished through the fluorinated ligand, which serves to insulate the analyte from the thermal energy of the AuNP (∼2000K) while the laser induced release of the ligand allows it to act as a conduit for analyte desorption. We posit that the thermal desorption of the ligand provides enough kinetic energy to drive analyte desorption into the gas phase with minimal energy input, as illustrated in Figure 1.

Figure 1. Decoupling laser induced nanoparticle heating from desorption/ionization.

Schematic illustration of the possible desorption mechanism: upon irradiation, gold core efficiently absorbs the laser energy, and transfers the energy to thermally release fluorinated ligands. The desorbed fluorinated ligands provide the kinetic energy (and driving force) for analyte desorption, and serve to protect the analyte from thermal degradation. Protonated diacetylspermine is shown as an example of f-AuNP desorption/ionization.

In a representative experiment we have demonstrated the utility of these f-AuNPs to carry out MS analysis of pure standards (Supplementary Figure 1) and human plasma (Supplementary Figure 2) using two instruments designed for MALDI, an AB SCIEX TOF/TOF 5800 and a Waters Synapt G2. AuNPs also offer a straight-forward platform for functionalization using gold-thiol chemistry. Here we used two separate commercially available thiols, 1H,1H,2H,2H-perfluorodecanethiol (fC10) and 1H,1H,2H,2H-perfluorooctanethiol (fC8). However, there is also the opportunity to design new ligands for the AuNPs that could enhance ionization, for example amine fluorocarbon ligands could facilitate desorption/ionization of negatively charged metabolites since the ligand's amine would act as a proton acceptor.

Soft Ionization with Fluorinated Gold Nanoparticles

To illustrate the laser induced thermal energy generated at f-AuNPs, 4nm f-AuNPs were measured with TEM before and after laser irradiation (Figure 2). The size distribution in the top panel of Figure 2 shows an increase in size (to ∼6nm) indicating that the particles melt and anneal following exposure to the laser pulses. The accompanying TEM images in Figure 2b offer further evidence that laser radiation has melted and fused the f-AuNPs. The thermal energy responsible for melting the particles can be used to desorb the fluorocarbon ligand, thus indirectly desorbing analyte molecules into the gas phase for mass spectrometry analysis. Thermal desorption, however, typically requires high energy, which leads to significant fragmentation, including formation of ions that are primarily cation adducts³³ and the formation of gold cluster ions³⁷. Therefore, our next set of experiments explored the performance of the f-AuNPs and whether thermal release of the fluorocarbon ligand was beneficial to the mass spectrometry analyses. To do this the f-AuNPs were compared to MALDI and gold nanoparticles functionalized with the nonfluorous ligand octanethiol (C8-AuNPs) by tracking the survival yield of the thermally labile molecule methoxybenzyl pyridinium (mBP) with respect to laser energy (Figure 2). Survival yield was calculated as the ratio of [M]⁺ (m/z = 200) to the major fragment at m/z = 121. Desorption of mBP was initiated at energies above 0.78 μJ; when using MALDI with α-cyano-4-hydroxycinnamic acid, (C8-AuNP) initiated desorption at energies above 0.50 μJ while the f-AuNP initiated desorption at energies above 0.25 μJ for the 8 carbon fluorous ligand (F8-AuNP) and 0.34 μJ for the 10 carbon fluorous ligand (F10-AuNP). The low energy behavior of f-AuNPs allows NIMS experiments to be carried out at energies that are below the threshold for gold cluster formation (Supplementary Figure 3), a significant advantage since these ion clusters can complicate the mass spectrum in the low mass region. In addition the low energies used tend to create minimal background signal compared to typical MALDI matrices (Supplementary Figure 4-15).

Figure 2. Soft Ionization with Fluorinated Gold Nanoparticles.

(a) The diameter of AuNPs increases from 3.5 ± 0.5 nm to 6.0 ± 1.4 nm after laser irradiation. (b) Transmission electron microscopy (TEM) images of AuNPs before and after laser irradiation. Scale bar = 10 nm. (c) Survival yield vs. laser energy plot of mBP for F8-AuNP, F10-AuNP, C8-AuNP and MALDI (error bars are standard deviation). (d) Signal-to-noise vs. laser energy plot for [M]⁺ (m/z = 200) for F8-AuNP, F10-AuNP, C8-AuNP and MALDI (error bars are standard deviation).

The survival yield plot in Figure 2 shows that the f-AuNPs performed exceptionally well in terms of fragmentation as compared to the C8-AuNPs. We observed that fragmentation begins immediately at the threshold energy required for desorption and levels out at approximately 20% survival for C8-AuNP whereas the F8-AuNP maintained 100% survival over 0.25-0.50 μJ and reached a steady state of 60% at 1.25 μJ. These results suggest that the fluorous-thiol functionality effectively insulates the sample from the potentially damaging thermal energy from the irradiated gold nanoparticles. This is further evidenced by the observation that the longer fluorinated alkane thiol functionalized F10-AuNPs maintain 100% survival over a longer range (0.34-0.80 μJ) as presumably the longer chain better insulates the analyte from the heat generated at the particle surface. It is also interesting to note that fragmentation begins at energies far below the threshold for desorption of bare nanoparticles, showing the inherent harshness of nanoparticle based thermal desorption. The comparison to be made with MALDI-MS is more nuanced, at very low energies desorption does not occur in MALDI-MS while it does occur using f-AuNP with essentially no damage to the molecular ion. As the energy approaches the threshold for MALDI, the survival yield for f-AuNPs begins to decrease and continues to decrease at a slower rate than MALDI until both desorption methods reach a steady state of 60% at 1.25 μJ.

Generally, we observed that the f-AuNPs outperform MALDI at low energy and perform comparably at higher energies. The signal-to-noise ratios plotted in Figure 2 show that the particles perform better than both MALDI and the C8-AuNP in terms of the generation of [M]⁺ signal. This result is again most likely due to the low energy requirements for this type of desorption/ionization. Additionally the longer chain appears to perform slightly better than the shorter chain. The length of the chain appears to shift and extend the optimal energy range for this experiment, however in both cases it should be noted that the maximum signal-to-noise occurs at energies above 100 % survival. Furthermore it could be the case the trend would continue with the use of a perfluorododecanethiol (F12) however this ligand was not readily available.

In addition to the low energy requirements of the f-AuNP observed in the survival yield experiments, SEM data indicates that the desorption process is particularly soft. Unlike the typical ablation “craters” observed in MALDI-MS analysis of tissue (Supplementary Figure 16) we observed plateau-like structures in the f-AuNP experiments. Figure 3 shows a slice of lung tissue that was spotted with the f-AuNP solution and irradiated with a Nd:YAG laser. In the treated area the laser pulses create raised protrusions. Outside of this f-AuNP coated region no protrusions were formed. Interestingly laser pulses that occurred at the interface create partial plateau structures. We suspect that the protrusion of the surface following laser radiation is a side product brought about by the heating of the f-AuNPs. We speculate that the heat of the f-AuNPs vaporizes the more volatile components in the tissue, creating the plateau like effect, however this phenomenon requires further investigation.

Figure 3. Characterization of desorption/ionization using fluorinated nanoparticles.

(a) Silicon substrate with a thaw-mounted section of mouse lung spotted with a f-AuNP solution. (b) Scanning electron microscopy (SEM) characterization of the mouse lung section spotted with f-AuNPs after laser irradiation. (c) The plateau shaped spots (50-60 μm in diameters) formed on the tissue surface after laser irradiation.

NIMS and SEM imaging of biofilms

The overarching goals of this technology are to increase both the accessibility and the functionality of nanostructure-based imaging. Using f-AuNPs as a platform accomplishes these goals by adding multiple methods of imaging capabilities. To this point, another advantage of f-AuNPs is their solubility in biologically inert fluorocarbon solvents that can be applied to the top of a tissue sample. This contrasts to classic silicon NIMS experiments, which require that the sample be thinly sliced and placed on top of a nanostructured surface. We tested the versatility of the f-AuNPs on a biofilm sample that would not be immediately accessible to silicon nanostructure-based techniques due to the thickness of the sample³⁸. To analyze these samples, the aclar substrates that the biofilms were grown on were attached directly to the target plate where, following desiccation, the f-AuNPs were deposited drop wise.

The NIMS data shown in Figure 4 illustrates that f-AuNP can be used to initiate desorption/ionization from these irregular biofilm surfaces. This image compares two biofilm cultures of Desulfovibrio vulgaris (DVH); one that was grown in balanced conditions and one that was grown in stressed conditions. Stressed conditions refer to an electron acceptor limited (EAL) environment, which affects the biofilm growth of sulfate reducing bacteria, like DVH. The mass spectra extracted from the balanced and stressed bacteria (Figure 4) show several differences, the most dramatic one at m/z 551, which has been mapped to the right of the mass spectra in Figure 4. This ion was putatively identified (Supplementary Figure 17 & Supplementary Table 1) diglyceride (16:0/16:0)³⁹ and might be indicative of perturbed metabolism in the stressed bacteria, however this is still a very preliminary finding. Additionally f-AuNPs were successfully applied to the bacteria sample, following fixation and dehydration, to act as a contrast agent for the comparatively high resolution SEM images shown in Figure 4. Surprisingly, we found that the density of the EAL bacteria was in fact increased relative to the balanced bacteria. This result was confirmed using a standard SEM procedure and is currently under further investigation.

Figure 4. NIMS and SEM imaging using fluorinated gold nanoparticles.

(a) Mass spectra generated from two regions of interest in the f-AuNP MSI, one corresponds to the biofilm grown in balanced media (blue) and one corresponding to the biofilm grown in electron acceptor limited (EAL) media (red). The inset (b) shows the ion image for m/z 551. (c) SEM images of balanced and stressed biofilms treated with f-AuNP.

NIMS and X-ray μCT imaging of mouse lung tissue

The success of the mass spectrometric detection of metabolites using f-AuNPs (Figure. 4) has allowed for the further integration of the f-AuNPs NIMS analysis with μCT. Together, these two modes of imaging allow for the correlation of 3-dimensional anatomical (structural) and molecular information (Supplementary Figure. 18). For example this has been demonstrated in the analysis of metastatic mouse lungs. Specifically, 500 μL of the biologically inert f-AuNP solution was intratracheally introduced into mouse lungs and immediately distributed into the lung tissue. The liquid ventilated lung was then embedded into OCT (optimal cutting temperature) material and preserved in -80 °C until analysis. The mouse lung was then imaged with μCT to construct high resolution 3-dimensional image (Figure. 5 Supplementary Video 1). F-AuNPs were well distributed into lung tissue and characterized the airway and porosity of the lung. The blood vessels appear as dark areas and the regions of the lungs carrying metastases revealed dark spots consistent with the exclusion of nanoparticle from the metastatic lesions (Supplementary Figure. 19).

Figure 5. NIMS and μCT imaging using fluorinated gold nanoparticles.

(a) Mass spectra generated from a single lobe metastatic mouse lung ventilated with f-AuNPs. The inset (b) shows the ion image for m/z 756. (c) μCT images of the same lobe of the f-AuNP ventilated metastatic mouse lung at 0° and 135° where gold indicates the surfaces of the f-AuNP ventilated lung and silver represents the volume.

To obtain molecular information from liquid ventilated metastatic lung tissue, OCT embedded lungs were sectioned (20 μm) and analyzed. Since the f-AuNPs solution had been passed through the trachea into the lung, no additional f-AuNPs were applied to the tissue. A mass spectrometry image of the f-AuNP ventilated left lobe of the lung is shown in Figure. 5. In general, mass spectrometry analysis is a multiplexed analysis where multiple molecular ions can be simultaneously detected in one experiment. Here, we chose to map a phosphatidylcholine (Supplementary Figure. 20) at m/z 756 to demonstrate molecular information and its distribution in this tissue (Figure. 5). To confirm that the areas lacking nanoparticle signal did contain cancerous tissue, metastases in an intact liquid ventilated mouse lung were identified by hematoxylin and eosin (H&E) staining and compared to an adjacent NIMS image (Supplementary Figure. 19). To better access these structures it might be possible to approach the metastases from the blood stream by perfusing the animal with a synthetic blood form of the f-AuNP or to coat the tissue following sectioning (Supplementary Figure. 21).

To enable NIMS and X-ray μCT imaging of blood vessels in situ we took advantage of fluorocarbons utility as a blood substitute^2,40. The f-AuNPs were dissolved in the fluorocarbon perfluordecalin, which was emulsified to approximate the only FDA approved fluorocarbon based blood substitute⁴⁰. The f-AuNP emulsion was perfused into the circulatory system to demonstrate the ability to obtain structural and chemical information from the circulatory system associated with the lung (Supplementary Figure. 22) as well the liver (Supplementary Figure. 23) of the mouse. Additionally, we also applied these imaging approaches to investigate the structural and chemical effects of hyperoxia on the lung tissue of juvenile mice (Supplementary Figure. 24 & 25).

NIMS for analysis of central carbon metabolites

The majority of central carbon metabolites are anionic, and thus are better suited for analysis in negative ion mode imaging mass spectrometry. One successful approach used for the in situ ionization and imaging of central carbon metabolites employs amine functionalized initiators³⁰ and MALDI matrices³¹. Presumably, these adjuvants work well because the basic amine group acts as a proton acceptor to promote M-H^- production. Thus, to enable the application of this imaging platform to the analysis of central carbon metabolites in negative ionization mode we have to enriched the fluorocarbon solvent with the basic initiator 1H,1H,2H,2H,3H,3H-perfluoroundecylamine (PFUA).

As it was not clear that the f-AuNPs would transfer the requisite energy to the initiator molecule needed to induce desorption/ionization, we tested the enriched f-AuNPs using standard mixture of nine metabolites in negative mode. A mass spectrum generated from this experiment is shown in Figure 6, in addition to the peaks for each individual metabolite we also observe a peak for Au^- and PO₄H₂^-. We attribute the emergence of these ions to the higher energy used in this experiment. The spectra in Supplementary Figure. 3 shows that under the standard operation energy of 1.4 μJ no Au ions are formed, the addition of PFUA however increased the energy requirement to approximately 2 μJ. Just as the energy threshold increases with chain length (Figure. 2), the incorporation of the PFUA shifted this threshold ever further by ostensibly adding a second barrier between the AuNP and the analyte. However even at this increased energy the enriched f-AuNPs performed well in negative ion mode.

Figure 6. NIMS for the analysis of central carbon metabolites.

(a) A mass spectrum for 9 metabolites in a standard mixture. (b-d) NIMS images of a sagittal slice of a mouse brain collected in negative ion mode. Each image is paired with (e-g) the structure of the identified metabolite and (h-j) tandem MS data that was collected using LC-MS/MS.

The enriched f-AuNPs were then used to demonstrate central carbon metabolite imaging in tissue using negative ionization mode. The enriched particles were applied to the top of a sagittal slice from one half of a bifurcated mouse brain after desiccation. In Figure. 6 we have mapped the ions corresponding to lactate glutamate and docosahexenoic acid. The presence of each mapped metabolite was then confirmed by LC-MS/MS analysis of the second half of the brain. Here we have demonstrated that this platform like Si based NIMS³⁰ has the ability to use specialized initiators to expand the number of metabolites that are amicable to mass spectrometry imaging.

Discussion

Fluorinated gold nanoparticles (f-AuNPs) were designed to facilitate nanostructure imaging mass spectrometry (NIMS) as well as act as contrast agents for EM and μCT. An important feature of the f-AuNPs is that they promote a gentle laser desorption/ionization mechanism facilitating intact molecular ion formation with little background interference or molecular ion fragmentation. The utility of gold nanoparticles for structural μCT measurements is well established but the primary advance of employing fluorinated ligands to these structures has allowed for structural data (μCT) to be combined for the first time with molecular mass spectrometry information (f-AuNPs NIMS). This multimodal imaging approach is particularly useful for performing mass spectrometry-based metabolite imaging, where correlating metabolite concentrations with anatomical structure is key to data interpretation. The fluorocarbon liquid component of the method affords versatility in the delivery of the agent, which can be carried out via direct coating, liquid ventilation or perfusion allowing analysis of morphologically diverse biological samples.

Methods

Chemicals

Octanethiol functionalized gold nanoparticles (2-4nm DLS, 2% w/v in toluene) and fluorinated ligands 1H,1H,2H,2H-perfluorodecanethiol (fC10) and 1H,1H,2H,2H-perfluorooctanethiol (fC8), methoxybenzyl pyridinium chloride, and perfluorodecalin were purchased from Sigma-Aldrich (St. Louis, MO, USA), and 10 % Gibco® Pluronic® F-68 was from Life technologies (Grand Island, NY) 1H,1H,2H,2H,3H,3H-perfluoroundecylamine was from santa cruz biotechnology (Dallas, TX).

Nanoparticle synthesis

Octanethiol functionalized gold nanoparticles were in toluene with a concentration of 20 mg/mL. 1 mL of octanethiol functionalized gold nanoparticles (20 mg) was added to ∼20 mL of ethanol to precipitate the AuNPs with centrifugation at 4000 rpm for 15 min. The precipitated AuNP were then washed with acetone, briefly sonicated, and centrifuged again. The cleaning procedure was repeated three times before being dissolved in 1 mL of hexane. The AuNP solution (1 μL) was then analyzed using LDI-MS to test for the presence of tetraoctyl ammonium bromide by monitoring the tetraoctyl ammonium ion (TOA) at m/z 466, which is commonly used as a phase transfer additive in nanoparticle synthesis. More acetone washes were conducted until TOA was not detected. An additional 1 mL of hexane and 400 μL of 1H,1H,2H,2H-perfluorooctanethiol (fC8) or 1H,1H,2H,2H-perfluorodecanethiol (fC10) were added and the vial was purged with nitrogen gas to remove air. The solution was stirred for one to three days until gold nanoparticles precipitated. The solvent was evaporated with nitrogen gas flow and nanoparticles were washed three times with hexane, three times with acetone, and two times with 1:1:1 methanol/acetone/water, respectively, to remove excess ligand and impurities. Following washing, the AuNP were dried in the oven (∼80°C) for several minutes and stored as a solid. Before use, the AuNP were dissolved in tetradecafluorohexane (PFH) at 3 mg/mL for mass spectrometry and electron microscopy analyses and 10 mg/mL in perfluorodecalin for mouse lung perfusion experiments.

Enriched f-AuNPs were made by 3 mg/mL f-AuNPs into 5 % 1H,1H,2H,2H,3H,3H-perfluoroundecylamine perfluorodecalin solution.

The blood substitute f-AuNP solution was made by combining 50% 20 mg/ml f-AuNP/prefluorodecilin and 50% Pluronic® F-68 (0.5%) in Milli-Q water. The immiscible solutions were sonicated for 5 minutes at 50% duty cycle with a probe sonicator.

Electron microscopy characterization

For transmission electron microscopy (TEM) imaging, fluorinated AuNPs were deposited on 400 mesh copper grids and characterized by a Philips CM100 electron microscope (FEI, Hillsborough, OR) at 80 kV. Images were collected using a Megaview III ccd camera (Olympus Soft Imaging Solutions GmbH, Münster, Germany). Fluorinated AuNPs deposited on copper grids were also irradiated with (355 nm, laser energy 6.6 μJ, 2000 shots), and then measured with TEM. For scanning electron microscopy (SEM) analysis, 10 μL of 3 mg/mL fluorinated AuNPs in PFH were first deposited onto mouse brain or lung tissue which was then irradiated by a laser with a predefined 250 μm step size. Subsequently, the samples were imaged with a Hitachi S-4800 SEM at 5 kV. SEM was done on biofilms from the same batch. Aclar slides with adhered biofilm were aldehyde fixed (2.5% wt/vol glutaraldehyde, 2.0% wt/vol paraformaldehyde, 0.05M sodium cacodylate buffer pH 7.0) overnight. Samples were rinsed with ddH₂O and ethanol dehydrated. Critical point drying was then carried on the samples using CO₂ and spotted with f-AuNP solution (1mg/mL). Samples were also viewed on a Hitachi S4800 SEM.

Bacterial strains and growth conditions

Desulfovibrio vulgaris RCH1 was obtained from Dr. Romy Chakraborty (Lawrence Berkeley National Lab), and was isolated from Cr-contaminated groundwater at the U.S. Department of Energy Hanford reservation. D. vulgaris RCH1 was grown in LS4D medium, which contains lactate as the carbon source and electron donor and sulfate as the electron acceptor.⁴¹ Lactate and sulfate concentrations were altered to create balanced and electron acceptor limited conditions. The balanced condition was defined as 60 mM sodium lactate and 30 mM sodium sulfate and the electron acceptor limited condition was defined as 50 mM sodium lactate and 10 mM sodium sulfate. D. vulgaris RCH1 was grown as a biofilm under continuous flow conditions in a modified Center for Disease Control (CDC) reactor. Exponential phase cells were inoculated into a reactor containing balanced or electron acceptor limited lactate-sulfate media (LS4D) and were grown in batch mode for 48 hours. Biofilms were grown at room temperature (20-23°C), with a dilution rate of 0.04^-hr, stirred at 60 rpm, and the headspace was continually purged with sterile N₂ gas to maintain anaerobic conditions. Coupons of aclar (7.8 mil thickness) (Electron Microscopy Sciences, Hatfield, PA) supported by glass slides were submerged in the reactor body as a surface for biofilm growth. Aclar coupons were removed from the reactor after 144, rinsed three times in ice-cold phosphate buffered saline, wicked dry, and flash frozen in liquid nitrogen. Samples were stored at -80°C until analysis.

Animals and microCT imaging

All animal work complied with National Institutes of Health and institutional guidelines (TSRI is AAALAC, International accredited). Female 11-week old CB17-Prkdc^SCID mice were euthanized by overdose of isoflurane before exsanguination by cutting the abdominal aorta. A small incision was performed in the trachea to insert a 20 gauge blunt needle, which was secured by a piece of suture. Approximately 500 μL of 10 mg/mL f-AuNP in PFH solution was then injected into the lungs up to full lung inflation. Intact lungs were immediately harvested, placed in OCT compound embedding medium, frozen in liquid nitrogen, and stored at -80 °C prior to analysis.

For the hyperoxia experiment the experimental group consisted of C57BL/6J P7 pups (7 days old) exposed to 75% oxygen for 5 days and returned to room air at P12 (12 days old pup). The control group consisted of age matched pups raised in normoxia (21% O2) for the same period. Pups were sacrificed at P12. As was the case with adult mice, the pups were euthanized by overdose of isoflurane before exsanguination by cutting the abdominal aorta. Ventilation of the f-AuNPs in this case was carried out directly via the mouth to the trachea. Approximately 250 μL of 10 mg/mL f-AuNP in perfluorodecalin solution was then injected into the lungs up to full lung inflation. Again, the intact lungs were immediately harvested, placed in OCT compound embedding medium, frozen in liquid nitrogen, and stored at -80 °C prior to analysis.

For the blood substitute experiment a male mouse (C57BL/6J, 24 days of age) was anesthetized with isoflurane and the heart was exposed. A 23 gauge needle attached by tubing to a syringe was inserted into the left ventricle, the right atria was pierced, and 40 ml saline was perfused through the animal at a rate of 3.1 ml/min to clear all of the blood. A three-way valve was switched so that 3 ml of the f-AuNP blood substitute was then pumped through the mouse at the same rate. The lung and liver were harvested and imbedded in OCT until μCT analysis.

The intact mouse lungs and liver were imaged by μCT (vivaCT 75; Scanco Medical AG; Basserdorf, Switzerland) in standard resolution using the following parameters: 55kVP, 145μA, 300-ms integration time, and 41-μm voxel size. The scanning protocol was programmed to acquire images via a rotating gantry, resulting in a total of 500 step-projections per scan. The projections were reconstructed with a matrix of 1024×1024 using Scanco's μCT Tomography V5.4C software. The 2D binary digital imaging communication (DICOM) files obtained from Scanco's software were later analyzed using 64-bit OsiriX v.3.9.2 (Pixmeo; Geneva, Switzerland) software.

Mass spectrometry analysis and imaging

For analysis of standard compounds, 0.5 μL of f-AuNP solution (3 mg/mL) was first deposited onto a p-type silicon chip and allowed to air dry. Then, 0.1-0.5 μL of standard compound solution was deposited on top of dried f-AuNP layer and dried under vacuum. An AB SCIEX TOF/TOF 5800 MS system was used for data collection. The instrument was operated at reflectron mode with a repetition frequency of 400 Hz and an accelerating voltage of 15 kV. Each sample spectrum was averaged from 400 laser shots.

Plasma was analyzed using a MALDI SYNAPT G2S (Waters, Milford, MA) equipped with a Nd:YAG laser (355 nm) with a repetition frequency of 1000 Hz and variable laser energy (8-10 μJ). Nitrogen was used in the ion mobility cell and the mobility experiments were collected with a variable wave velocity of 320 to 900 m/s for the 50 to 1200 m/z region.

Mouse lung and liver tissue treated with AuNPs was sliced with a Leica CM1900 cryostat to a thickness of 20 μm, and then thaw-mounted directly onto p-type silicon chip. The tissues were directly imaged by an AB SCIEX TOF/TOF 5800 MS system without additional sample preparation. Tissue slices were imaged with a 100 μm step size and each recorded mass spectrum resulted from the average of 400 laser shots. Representative sections of the cancer metastasized lungs were collected on Superfrost Plus slides and stained with hematoxylin and eosin using routine histological techniques.

LC-MS/MS

Lung tissue and biofilm samples were analyzed using RPLC/MS analysis in ESI positive mode. The extracts were analyzed on 6550 iFunnel QTOF mass spectrometer (Agilent Technologies) interfaced with 1200 series HPLC system (Agilent Technologies). For RPLC separation, 0.1% formic acid in water was used as mobile phase A and 0.1% formic acid in acetonitrile was used as mobile phase B. The metabolite extract was loaded on to a C18 column using 5% mobile phase B at a flow rate of 100 μl/min and resolved using a linear gradient of 5% B – 95 % B over 60 min.