Towards instantaneous cellular level bio diagnosis: laser extraction and imaging of biological entities with conserved integrity and activity

Mass Spectral Imaging to Map Plant-Microbe Interactions

Plant-microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.

Picosecond infrared laser driven sample delivery for simultaneous liquid-phase and gas-phase electron diffraction studies

Here, we report on a new approach based on laser driven molecular beams that provides simultaneously nanoscale liquid droplets and gas-phase sample delivery for femtosecond electron diffraction studies. The method relies on Picosecond InfraRed Laser (PIRL) excitation of vibrational modes to strongly drive phase transitions under energy confinement by a mechanism referred to as Desorption by Impulsive Vibrational Excitation (DIVE). This approach is demonstrated using glycerol as the medium with selective excitation of the OH stretch region for energy deposition. The resulting plume was imaged with both an ultrafast electron gun and a pulsed bright-field optical microscope to characterize the sample source simultaneously under the same conditions with time synchronization equivalent to sub-micrometer spatial resolution in imaging the plume dynamics. The ablation front gives the expected isolated gas phase, whereas the trailing edge of the plume is found to consist of nanoscale liquid droplets to thin films depending on the excitation conditions. Thus, it is possible by adjusting the timing to go continuously from probing gas phase to solution phase dynamics in a single experiment with 100% hit rates and very low sample consumption (<100 nl per diffraction image). This approach will be particularly interesting for biomolecules that are susceptible to denaturation in turbulent flow, whereas PIRL-DIVE has been shown to inject molecules as large as proteins into the gas phase fully intact. This method opens the door as a general approach to atomically resolving solution phase chemistry as well as conformational dynamics of large molecular systems and allow separation of the solvent coordinate on the dynamics of interest.

Infrared Laser Ablation Microsampling with a Reflective Objective

A Schwarzschild reflective objective with a numerical aperture of 0.3 and working distance of 10 cm was used for laser ablation sampling of tissue for off-line mass spectrometry. The objective focused the laser to a diameter of 5 μm and produced 10 μm ablation spots on thin ink films and tissue sections. Rat brain tissue sections 50 μm thick were ablated in transmission geometry, and the ablated material was captured in a microcentrifuge tube containing solvent. Proteins from ablated tissue sections were quantified with a Bradford assay, which indicated that approximately 300 ng of protein was captured from a 1 mm² area of ablated tissue. Areas of tissue ranging from 0.01 to 1 mm² were ablated and captured for bottom-up proteomics. Proteins were extracted from the captured tissue and digested for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for peptide and protein identification.

Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue

Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m². Rat brain tissue sections mounted on quartz microscope slides and ablated in transmission mode yielded 2 μg protein per mm² as quantified by the Bradford assay. Tissue areas ranging from 0.06 mm² to 1 mm² were ablated and the ejected material was collected for proteomic analysis. Extracted proteins were digested and the resulting peptides were analyzed by LC-MS/MS. The proteins extracted from the ablated areas were identified and the average number of identified proteins ranged from 85 in the 0.06 mm² area to 2400 in the 1 mm² area of a 50 μm thick tissue. In comparison to infrared laser ablation of equivalent sampled areas, both the protein mass and number of proteins identified using DUV laser ablation sampling were approximately four times larger.

Ablation Precision and Thermal Effects of a Picosecond Infrared Laser (PIRL) on Roots of Human Teeth: A Pilot Study Ex Vivo

BACKGROUND/AIM

Picosecond infrared laser (PIRL) was investigated regarding its possible therapeutic application in cutting dental roots.

MATERIALS AND METHODS

Extracted human teeth were processed in the root area by laser ablations followed by histological evaluation. Dentin adjacent to the cutting surface was evaluated morphometrically.

RESULTS

PIRL produced clearly defined cutting boundaries in dental roots. At the bottom of the cavity, the ablation surface became slightly concave. Heat development in this scantly hydrated tissue was considerable. We attributed the excess heating effects to heat accumulation due to multiple pulse overlap across a limited scan range imposed by tooth geometries.

CONCLUSION

Defined areas of the tooth root may be treated using the PIRL. For clinical translation, it would be necessary to improve beam delivery to facilitate beam steering for the intended oral application (e.g. by using a fiber) and identify optimal repetition rates/scan speeds combined with cooling techniques to minimize accumulated heat within ablation cavities.

MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics

A multimodal workflow for mass spectrometry imaging was developed that combines MALDI imaging with protein identification and quantification by liquid chromatography tandem mass spectrometry (LC-MS/MS). Thin tissue sections were analyzed by MALDI imaging, and the regions of interest (ROI) were identified using a smoothing and edge detection procedure. A midinfrared laser at 3-μm wavelength was used to remove the ROI from the brain tissue section after MALDI mass spectrometry imaging (MALDI MSI). The captured material was processed using a single-pot solid-phase-enhanced sample preparation (SP3) method and analyzed by LC-MS/MS using ion mobility (IM) enhanced data independent acquisition (DIA) to identify and quantify proteins; more than 600 proteins were identified. Using a modified database that included isoform and the post-translational modifications chain, loss of the initial methionine, and acetylation, 14 MALDI MSI peaks were identified. Comparison of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the identified proteins was achieved through an evolutionary relationships classification system.

RNA sampling from tissue sections using infrared laser ablation

RNA was obtained from discrete locations of frozen rat brain tissue sections through infrared (IR) laser ablation using a 3-μm wavelength in transmission geometry. The ablated plume was captured in a microcentrifuge tube containing RNAse-free buffer and processed using a commercial RNA purification kit. RNA transfer efficiency and integrity were evaluated based on automated electrophoresis in microfluidic chips. Reproducible IR-laser ablation of intact RNA was demonstrated with purified RNA at laser fluences of 3-5 kJ/m² (72 ± 12% transfer efficiency) and with tissue sections at a laser fluence of 13 kJ/m² (79 ± 14% transfer efficiency); laser energies were attenuated ∼20% by the soda-lime glass slides used to support the samples. RNA integrity from tissue ablation was >90% of its original RIN value (∼7) and the purified RNA was sufficiently intact for conversion to cDNA and subsequent qPCR assay.

Mass spectrometry-based intraoperative tumor diagnostics

In surgical oncology, decisions regarding the amount of tissue to be removed can have important consequences: the decision between preserving sufficient healthy tissue and eliminating all tumor cells is one to be made intraoperatively. This review discusses the latest technical innovations for a more accurate tumor margin localization based on mass spectrometry. Highlighting the latest mass spectrometric inventions, real-time diagnosis seems to be within reach; focusing on the intelligent knife, desorption electrospray ionization, picosecond infrared laser and MasSpec pen, the current technical status is evaluated critically concerning its scientific and medical practice.

Sampling of Tissues with Laser Ablation for Proteomics: Comparison of Picosecond Infrared Laser and Microsecond Infrared Laser

It was recently shown that sampling of tissues with a picosecond infrared laser (PIRL) for analysis with bottom-up proteomics is advantageous compared to mechanical homogenization. Because the cold ablation of tissues with PIRL irradiation is soft, proteins remain intact and even enzymatic activities are detectable in PIRL homogenates. In contrast, it was observed that irradiation of tissues with a microsecond infrared laser (MIRL) heats the tissue, thereby causing significant damage. In this study, we investigated the question if sampling of tissues with a MIRL for analysis of their proteomes via bottom-up proteomics is possible and how the results are different from sampling of tissues with a PIRL. Comparison of the proteomes of the MIRL and PIRL tissue homogenates showed that the yield of proteins identified by bottom-up proteomics was larger in PIRL homogenates of liver tissue, whereas the yield was higher in MIRL homogenates of muscle tissue, which has a significantly higher content of connective tissue than liver tissue. In the PIRL homogenate of renal tissue, enzymatic activities were detectable, whereas in the corresponding MIRL homogenate, enzymatic activities were absent. In conclusion, MIRL and PIRL pulses are suited for sampling tissues for bottom-up proteomics. If it is important for bottom-up proteomic investigations to inactivate enzymatic activities already in the tissue before its ablation, MIRL tissue sampling is an option, because the proteins in the tissues are denatured and inactivated by the heating of the tissue during irradiation with MIRL irradiation prior to the ablation of the tissue. This heating effect is absent during irradiation of tissue with a PIRL; therefore, sampling of tissues with a PIRL is a choice for purifying enzymes, because their activities are maintained.

Infrared laser ablation and capture of enzymes with conserved activity

Infrared (IR) laser ablation at 3 μm wavelength was used to extract enzymes from tissue and quantitatively determine their activity. Experiments were conducted with trypsin, which was ablated, captured and then used to digest bovine serum albumin (BSA). BSA digests were evaluated using matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) and sequence coverage of 59% was achieved. Quantification was performed using trypsin and catalase standards and rat brain tissue by fluorescence spectroscopy. Both enzymes were reproducibly transferred with an efficiency of 75 ± 8% at laser fluences between 10 and 30 kJ/m². Trypsin retained 37 ± 2% of its activity and catalase retained 50 ± 7%. The activity of catalase from tissue was tested using three consecutive 50 μm thick rat brain sections. Two 4 mm² regions were ablated and captured from the cortex and cerebellum regions. The absolute catalase concentration in the two regions was consistent with previously published data, demonstrating transfer of intact enzymes from tissue.

Soft Picosecond Infrared Laser Extraction of Highly Charged Proteins and Peptides from Bulk Liquid Water for Mass Spectrometry

We report the soft laser extraction and production of highly charged peptide and protein ions for mass spectrometry directly from bulk liquid water at atmospheric pressure and room temperature, using picosecond infrared laser ablation. Stable ion signal from singly charged small molecules, as well as highly charged biomolecular ions, from aqueous solutions at low laser pulse fluence (∼0.3 J cm^-2) is demonstrated. Sampling via single picosecond laser pulses is shown to extract less than 27 pL of volume from the sample, producing highly charged peptide and protein ions for mass spectrometry detection. The ablation and ion generation is demonstrated to be soft in nature, producing natively folded proteins ions under sample conditions described for native mass spectrometry. The method provides laser-based sampling flexibility, precision and control with highly charged ion production directly from water at low and near neutral pH. This approach does not require an additional ionization device or high voltage applied directly to the sample.

Protein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallography

In order to utilize the high repetition rates now available at X-ray free-electron laser sources for serial crystallography, methods must be developed to softly deliver large numbers of individual microcrystals at high repetition rates and high speeds. Picosecond infrared laser (PIRL) pulses, operating under desorption by impulsive vibrational excitation (DIVE) conditions, selectively excite the OH vibrational stretch of water to directly propel the excited volume at high speed with minimized heating effects, nucleation formation or cavitation-induced shock waves, leaving the analytes intact and undamaged. The soft nature and laser-based sampling flexibility provided by the technique make the PIRL system an interesting crystal delivery approach for serial crystallography. This paper demonstrates that protein crystals extracted directly from aqueous buffer solutionviaPIRL-DIVE ablation retain their diffractive properties and can be usefully exploited for structure determination at synchrotron sources. The remaining steps to implement the technology for high-speed serial femtosecond crystallography, such as single-crystal localization, high-speed sampling and synchronization, are described. This proof-of-principle experiment demonstrates the viability of a new laser-based high-speed crystal delivery system without the need for liquid-jet injectors or fixed-target mounting solutions.

Chemical Printing of Biological Tissue by Gold Nanoparticle-Assisted Laser Ablation

A chemical printing method based on gold nanoparticle (AuNP)-assisted laser ablation has been developed. By rastering a thin layer of AuNPs coated on a rat kidney tissue section with a UV laser, biomolecules are extracted and immediately transferred/printed onto a supporting glass substrate. The integrity of the printed sample is preserved, as revealed by imaging mass spectrometric analysis. By studying the mechanism of the extraction/printing process, transiently molten AuNPs were found to be involved in the process, as supported by the color and morphological changes of the AuNP thin film. The success of this molecular printing method was based on the efficient laser-nanomaterial interaction, that is, the strong photoabsorption, laser-induced heating, and phase-transition properties of the AuNPs. It is anticipated that the molecular printing method can be applied to perform site-specific printing, which extracts and transfers biochemicals from different regions of biological tissue sections to different types of supporting materials for subsequent biochemical analysis with the preservation of the original tissue samples.

Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution

Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 10⁷ V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 10¹⁰ V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

Comparative study of wound healing in rat skin following incision with a novel picosecond infrared laser (PIRL) and different surgical modalities

Background and Objective

As a result of wound healing the original tissue is replaced by dysfunctional scar tissue. Reduced tissue damage during surgical procedures beneficially affects the size of the resulting scar and overall healing time. Thus the choice of a particular surgical instrument can have a significant influence on the postoperative wound healing. To overcome these problems of wound healing we applied a novel picosecond infrared laser (PIRL) system to surgical incisions. Previous studies indicated that negligible thermal, acoustic, or ionization stress effects to the surrounding tissue results in a superior wound healing.

Study Design/Materials and Methods

Using the PIRL system as a surgical scalpel, we performed a prospective wound healing study on rat skin and assessed its final impact on scar formation compared to the electrosurgical device and cold steel. As for the incisions, 6 full‐thickness, 1‐cm long‐linear skin wounds were created on the dorsum of four rats using the PIRL, an electrosurgical device, and a conventional surgical scalpel, respectively. Rats were euthanized after 21 days of wound healing. The thickness of the subepithelial fibrosis, the depth and the transverse section of the total scar area of each wound were analyzed histologically.

Results

After 21 days of wound healing the incisions made by PIRL showed minor scar tissue formation as compared to the electrosurgical device and the scalpel. Highly significant differences (P < 0.001) were noted by comparing the electrosurgical device with PIRL and scalpel. The transverse section of the scar area also showed significant differences (P = 0.043) when comparing PIRL (mean: 141.46 mm²; 95%CI: 105.8–189.0 mm²) with scalpel incisions (mean: 206.82 mm²; 95%CI: 154.8–276.32 mm²). The subepithelial width of the scars that resulted from using the scalpel were 1.3 times larger than those obtained by using the PIRL (95%CI: 1.0–1.6) though the difference was not significant (P < 0.083).

Conclusions

The hypothesis that PIRL results in minimal scar formation with improved cosmetic outcomes was positively verified. In particular the resection of skin tumors or pathological scars, such as hypertrophic scars or keloids, are promising future fields of PIRL application. Lasers Surg. Med. 48:385–391, 2016. © 2016 The Authors. Lasers in Surgery and Medicine Published by Wiley Periodicals, Inc.

Homogenization of tissues via picosecond-infrared laser (PIRL) ablation: Giving a closer view on the in-vivo composition of protein species as compared to mechanical homogenization

Posttranslational modifications and proteolytic processing regulate almost all physiological processes. Dysregulation can potentially result in pathologic protein species causing diseases. Thus, tissue species proteomes of diseased individuals provide diagnostic information. Since the composition of tissue proteomes can rapidly change during tissue homogenization by the action of enzymes released from their compartments, disease specific protein species patterns can vanish. Recently, we described a novel, ultrafast and soft method for cold vaporization of tissue via desorption by impulsive vibrational excitation (DIVE) using a picosecond-infrared-laser (PIRL). Given that DIVE extraction may provide improved access to the original composition of protein species in tissues, we compared the proteome composition of tissue protein homogenates after DIVE homogenization with conventional homogenizations. A higher number of intact protein species was observed in DIVE homogenates. Due to the ultrafast transfer of proteins from tissues via gas phase into frozen condensates of the aerosols, intact protein species were exposed to a lesser extent to enzymatic degradation reactions compared with conventional protein extraction. In addition, total yield of the number of proteins is higher in DIVE homogenates, because they are very homogenous and contain almost no insoluble particles, allowing direct analysis with subsequent analytical methods without the necessity of centrifugation.

Biological significance

Enzymatic protein modifications during tissue homogenization are responsible for changes of the in-vivo protein species composition. Cold vaporization of tissues by PIRL-DIVE is comparable with taking a snapshot at the time of the laser irradiation of the dynamic changes that occur continuously under in-vivo conditions. At that time point all biomolecules are transferred into an aerosol, which is immediately frozen.

Ambient Mass Spectrometry Imaging with Picosecond Infrared Laser Ablation Electrospray Ionization (PIR-LAESI)

A picosecond infrared laser (PIRL) is capable of cutting through biological tissues in the absence of significant thermal damage. As such, PIRL is a standalone surgical scalpel with the added bonus of minimal postoperative scar tissue formation. In this work, a tandem of PIRL ablation with electrospray ionization (PIR-LAESI) mass spectrometry is demonstrated and characterized for tissue molecular imaging, with a limit of detection in the range of 100 nM for reserpine or better than 5 nM for verapamil in aqueous solution. We characterized PIRL crater size using agar films containing Rhodamine. PIR-LAESI offers a 20-30 μm vertical resolution (∼3 μm removal per pulse) and a lateral resolution of ∼100 μm. We were able to detect 25 fmol of Rhodamine in agar ablation experiments. PIR-LAESI was used to map the distribution of endogenous methoxykaempferol glucoronide in zebra plant (Aphelandra squarrosa) leaves producing a localization map that is corroborated by the literature. PIR-LAESI was further used to image the distribution inside mouse kidneys of gadoteridol, an exogenous magnetic resonance contrast agent intravenously injected. Parallel mass spectrometry imaging (MSI) using desorption electrospray ionization (DESI) and matrix assisted laser desorption ionization (MALDI) were performed to corroborate PIR-LAESI images of the exogenous agent. We further show that PIR-LAESI is capable of desorption ionization of proteins as well as phospholipids. This comparative study illustrates that PIR-LAESI is an ion source for ambient mass spectrometry applications. As such, a future PIRL scalpel combined with secondary ionization such as ESI and mass spectrometry has the potential to provide molecular feedback to guide PIRL surgery.