The authors would like to thank Clemson University, COMSET and Clemson SC BioCRAFT. The XELCI setup was initially developed with funds from NSF CAREER CHE 12255535 and later by NIH NIAMS R01 AR070305-01.

This procedure follows the animal use protocols approved by the Clemson University Institutional Animal Care and Use Committee (IACUC). The experiments are carried out according to the Clemson University Biosafety Committee (IBC) and radiation safety committee (RSC) as well as following the relevant guidelines and regulations.
NOTE: A flow diagram of completing a XELCI scan is shown below in Figure 5 followed by a detailed step-by-step description of the imaging procedure.
1. Initialize the system and acquire a plain radiograph
<ol>
	<li>Turn on PMT cooler, it typically takes ~15 min to reach the setpoint (e.g., 4 &#176;C). Perform the rest of the initialization steps before turning on the PMTs.</li>
	<li>Open the imaging system controlling software. The controlling software program communicates and initializes the x-y-z axis motorized stage. Move the stage x-axis and y-axis to the desired starting position.</li>
	<li>Place the sample on the movable x-y-z stage. Position the sample height (z-axis), so the radioluminescent device is 5-5.5 cm below the polycapillary focus optics by raising or lowering the X-ray source and/or the stage. Also, position the specimen in the x-y plane with the help of the laser crosshead (two red line-shaped laser pointers attached to the X-ray focusing capillary and positioned at 90&#176; to each other so that the lines intersect where the X-ray will focus). Turn off the lasers before X-rays and PMTs are turned on.</li>
	<li>Secure the push button interlock at the front door of the imaging enclosure. Turn on the power for the-ray source. Remove the focusing optics for obtaining the plain radiograph of the sample.</li>
	<li>Open the X-ray controlling software and set the X-ray power (by adjusting voltage and current). Open the X-ray shutter with the X-ray controlling software.</li>
	<li>Open the software for X-ray camera. Hit the exposure button to take the plain radiograph. Turn off the exposure and turn off the X-ray. 
	NOTE: If needed, move the sample to improve sample position or acquire a series of X-rays at different positions so they can be collated to get a larger radiograph view. One can also acquire a radiograph on a separate system, but co-registration between XELCI and radiography becomes more difficult if the specimen moves.</li>
	<li>Open the enclosure door.</li>
</ol>
2. Optionally, perform a background scan with the X-ray off
<ol>
	<li>Connect the polycapillary optics again to the X-ray source.</li>
	<li>Close the enclosure and secure the interlock. Turn on the PMT power supply. 
	NOTE: The PMT power supply should always be turned off whenever the door is open or about to be opened to avoid overexposure to light.</li>
	<li>Open the imaging system controlling software and specify the step size, scan speed, and scan area. Once all the parameters are set, start the scan by hitting the Run button. 
	NOTE: For a high-resolution scan, the step size will be 1000 &#181;m and for a low-resolution scan, the step size will be 250 &#181;m. The scan speed can be chosen from 5 mm/s through the 1 mm/s. The area of the scan depends on the dimensions of the sample.</li>
	<li>Run a background scan with the X-ray off to determine the dark counts from any light present in the enclosure other than the sample.</li>
</ol>
3. Perform a sample scan with the X-ray on
<ol>
	<li>Ensure the sample is still in the correct position with the laser cross head to begin the scan.</li>
	<li>Close the enclosure and secure the interlock. If the PMTs are off (e.g., turned off prior to opening the door), turn on the PMT power supply.</li>
	<li>Open the imaging system controlling software. Enter the values for step size, scan speed, and scan area. Once all the parameters are set, Hit the Run button to start the scan. 
	NOTE:&#160;For a high-resolution scan, the step size will be 1000 &#181;m and for a low-resolution scan, the step size will be 250 &#181;m. The scan speed can be chosen from 5 mm/s through the 1 mm/s. The area of the scan depends on the dimensions of the sample.</li>
	<li>Obtain the scan for the sample with the X-ray on.</li>
	<li>First, perform the low-resolution scan with larger step sizes and higher scan speed to obtain a preliminary image of the target. After obtaining a low-resolution scan of the desired area of the sample, obtain the higher resolution scan with a smaller step size and lower scan speed.</li>
	<li>Turn off the PMT power supply prior to opening the door.</li>
</ol>
4. Forming the image
<ol>
	<li>Validate the current scan is imaging the area of interest of the target. If not, stop the current scan by hitting the Stop button.</li>
	<li>Adjust the scanning positions in the controlling software again and hit the Run button again. 
	&#8203;NOTE: The y-axis is continuously recorded starting from the first row of the scan. While performing a scan, the number of counts per each wavelength and time since the last updated motor position is recorded. The time recorded will account for any changes in motor speed, thus the exposure time. For each pixel, counts/second is normalized. The y-axis motor travels to scan the end of the current row of the y-axis and the motor comes back to the starting position. Then the x-axis motor increases its position by a step size defined by the user and scans the second row of the y-axis. This process is cycled until the x-axis motor reaches the specified width for the x-direction. The user can control the scan size, motor speed, and motor starting positions. The step size will determine the size of the pixels in the final image of the y-axis.</li>
</ol>
5. Culturing bacteria for imaging in sterile conditions (If bacterial grown sensors are imaged)
<ol>
	<li>To prepare a fresh culture of Staphylococcus aureus 1945 (ATCC 25923), use one colony from a TSA (Tryptic soy agar) plate streaked within 1 week to inoculate 5 mL of sterile Tryptic Soy Broth (TSB).</li>
	<li>Shake the bacterial culture gently at 37 &#176;C for 16-18 h until the stationary phase.</li>
	<li>Next, pellet the culture from the TSB via centrifugation at 4000 x g for 10 min at room temperature (RT) and wash the pellet twice with Phosphate Buffer Solution (PBS) and resuspend the pellet in 5 mL of sterile PBS.</li>
	<li>Quantify the bacterial concentration using optical density at 600 nm using the linear range, which is the OD range where the Beer-Lambert law is verified (OD = kN; k is a coefficient relative to the molecular extinction and the length of the optical path, N is the bacterial concentration)16. Then dilute the sample to 105 cells/mL using sterile PBS.</li>
	<li>Sterilize the Tryptic Soy Agar (TSA) by autoclaving and then cool by mixing until the temperature reaches 45 &#176;C. Inoculate the bacteria into the TSA.</li>
	<li>Pipette the diluted bacterial culture (100 &#181;L) onto the surface of the implantable sensor. 
	NOTE: Implants were sterilized by immersion in 70% ethanol for 5 min and stored in sterile PBS.</li>
	<li>Pipette 100 &#181;L of uninoculated TSA over another sterile implant as a control</li>
	<li>Add an additional 100 &#181;L of uninoculated TSA over the implantable sensor before it is incubated at 37 &#176;C for 48 h prior to implantation.</li>
</ol>

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The authors claim no conflicts of interest.

To be able to detect and study orthopedic implant-associated infections early to avoid complications from osteomyelitis and secondary surgical procedures, we have introduced XELCI as a novel, functional imaging technique. It is comparable with the currently available techniques for pH monitoring through tissue.
While positioning the sample for imaging, we use a laser cross head connected to polycapillary focusing optics with two intersecting line-shaped laser pointers at the 90&#176; angle to ...

In the United States, about 2 million fracture fixation devices are inserted annually, and 5%-10% of them lead to implant-associated infections1. These infections are harder to treat with antibiotics at later stages due to the heterogeneity and antibiotic-resistant nature of the biofilms2,3. If they are diagnosed early, infections can be treated with antibiotics and surgical debridement to prevent extra medical costs for a second surgery to replace hardware at the treated fracture site. Plain radiography and other advanced radiographic techniques are applied in the diagnosis of orthopedic implant-associated infections, non-unions, and related complications. Although these techniques are used frequently to acquire structural information of the surrounding bone and tissue at the orthopedic implant, they are unable to provide biochemical information in the specific environment. Thus, we developed a novel X-ray excited luminescence chemical imaging (XELCI) technique for high-resolution imaging of biochemical information noninvasively at the implant site. Diagnosis of orthopedic implant-associated infections is commonly carried out by one or a combination of different means. Clinical observations (pain, swelling, redness, wound discharge, etc.) suggest the first signs of infection. Later, radiological and laboratory experiments are carried out to confirm the failure of bone healing progression and identify the pathogenic organism4,5. Nuclear medicinal techniques such as computerized tomography (CT), magnetic resonance imaging (MRI), and radionucleotide methods such as Single Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET) are in use for better visualization of the infected implant and the associated infection6,7. CT and MRI are advantageous in determining bone necrosis and soft tissue abnormalities, respectively but cause interferences at a close distance to the metal implants8. Different X-ray methodologies such as SPECT and PET in combination with radioisotope-labeled analytes as in vivo imaging contrast agents are widely utilized to diagnose implant-associated osteomyelitis2. Current applications combine both data from CT scanning and labeling data from either SPECT or PET to generate anatomical information9. Although one or more of these imaging modalities are used to aid infection diagnosis, they cannot detect the pH variations associated with infection early to initiate the treatments with antibiotics to avoid extra medical and surgical expenses.
The main advantage of utilizing the imaging system used in this study for monitoring implant-associated infections is its ability to reveal biochemical information about the biofilm microenvironment with a spectral reference. Although the main focus is on imaging and mapping pH at the infected site, this method can be altered to monitor other biomarkers specific to implant-associated infections. Thus, XELCI allows understanding the pathophysiology of the infection. The high spatial resolution imaging allows mapping heterogeneity as the infection grows. pH at the surface where the biofilm formation occurs is very important to understanding biochemical changes. Also, other microenvironment changes can occur due to antibiotic-related stress responses by bacteria10,11. Due to surface-specific and high spatial resolution imaging, the antibiotic effect on the biofilm microenvironment can be monitored. The technique can also be used to study the biofilm environment for targeted drug delivery experiments. We can study targeted low pH drug release or raising pH to make them more susceptible to work at higher pH.
Three specific characteristics of this imaging technique are X-ray resolution, Implant surface specificity, and chemical sensitivity (Figure 1A). These characteristics can be compared with the currently available imaging techniques for imaging orthopedic implant-related infections (Figure 1B). Once irradiated with X-rays, phosphor particles coated on the implant surface generate red and near-IR (NIR) light that can penetrate through a few centimeters of tissue (albeit with some attenuation)12,13. Table 1 shows some of the features of the developed imaging system compared to other ways that have been used to measure pH in biofilms or through tissue.
XELCI is a novel imaging technique to acquire high spatial resolution chemical information optically near implanted medical devices in combination with X-ray excitation, as shown in Figure 2. Here the selective excitation and optical detection of X-ray excitable phosphor particles is utilized. The implant is coated with two layers, a pH-sensitive dye incorporated polymer layer over a layer of scintillator particles. Once a sequence of focused X-ray beams irradiates the implant, the scintillator layer generates visible light (620 nm and 700 nm). This produced light passes through the pH-sensitive layer modulating the luminescence spectrum depending on the pH of the surrounding environment. Low pH is generally associated with infection and biofilm formation; as the infection progresses, the pH changes from physiological pH (pH 7.2) to acidic (less than pH 7), and the pH dye in the sensor changes color and thus absorbance. The variation of the luminescence spectrum is shown in Figure 2E for Bromocresol green pH dye at pH 7 and pH 4. The transmitted light through tissue and bone is collected and the spectral ratio determines pH. To generate a pH image, the focused X-ray beam irradiates a point at a time in the scintillator film and scans the beam point-by-point across the sample. Previously, this technique was applied to image pH variation on the surface of the orthopedic implants14,15 and have tested it to monitor pH variations in the intramedullary canal through bone and tissue.
Figure 3 below shows a schematic of the imaging system. Basic components of the imaging system are the X-ray excitation source with poly capillary optics, a one-piece acrylic light guide connecting to two photomultiplier tubes, the x, y, and z motorized stage (30 cm x 15 cm x 6 cm travel) and the computer connected for data acquisition. The X-ray source, x,y,z stage, and collection optics (elbow, light guide, photomultiplier tubes (PMTs)) are in the X-ray proof enclosure, while the X-ray controller, power source for PMTs, function generator connected to the data acquisition (DAQ) board and computer are kept outside. A push-button, normally open switch, placed between the enclosure and the front of the door serves as an interlock. If the door is not fully closed (the interlock switch is open), the X-ray source will not turn on, and it will automatically turn off the X-ray source if it is opened during operation. The motors can execute a continuous scan as well as they can be moved to any discrete location. The scan speed for y-axis is usually 1-5 mm/s, while the step size on the x-axis can be chosen typically from 150-2000 &#181;m. The parameters can be chosen depending on the required spatial resolution. Even exposure times are confirmed by consistent speed throughout a continuous scan.
Once the focused X-ray beam is irradiated on the X-ray luminescence particles, the generated light will pass through the pH-sensitive film by modulating the light depending on the surrounding pH. The transmitted light will interact (scatter and absorb partially) with a tissue, while the light attenuation by scattering and absorption will increase as the tissue thickness increases. The collection optics includes a one-piece bifurcated acrylic light guide fitted with a reflective aluminum elbow (with a&#160;90&#176; bend and polished reflective interior surface) at the beginning. This is to ensure the light is collimated as soon as light reaches the light guide. These additions significantly improved the light collection efficiency. For further details, Figure 4 shows the machine drawings of the elbow and light guide. The 90&#176; elbow was machined out of aluminum with the internal surface polished to a mirror finish and the light guide was machined with Acrylic. We have also attached a broad range long-pass blue light filter (blocking 350-450 nm light) at the beginning of the elbow to ensure that only red light will pass through. The end of the one-piece acrylic light guide bifurcates into two streams leading to two different PMTs. The PMTs are enclosed in a small light-tight metal box that is in contact with a thermoelectric cooler to cool down the PMTs to ~5 &#176;C. At the beginning of one of the PMTs, a narrow range long-pass filter (blocking 570-640 nm light and passing 640-740 nm light) is attached to measure only the 700 nm light. Therefore, the 620 nm and 700 nm light can be calculated separately. The PMTs are set up in photon counting mode, and they generate transistor-transistor logic (TTL) pulses for each photon detected. A DAQ system counts the pulses (saturation point 20 million pulses per second) using USB communication. Two separate intensity maps are generated after processing the data, and a final image is created by considering the ratio of the signal wavelength intensity (620 nm) to the reference wavelength intensity (700 nm). This ratio accounts for differences in total light collection efficiency, which depend strongly on the position of collection optics, X-ray irradiation intensity, and tissue thickness. In addition, a spatially separated reference region without any pH indicator dye accounts for spectral distortion from wavelength-dependent tissue penetration. A graphics-based programming language is used for controlling the imaging system, and a basic flow chart of the operation is shown below. The imaging setup, except for the computer, X-ray controller, and DAQ unit, is enclosed in a safe X-ray enclosure to minimize radiation exposure.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>90 degree elbow</td>
			<td>Produced in Hilltop Technology Laboratory, 51 Parker, Irvine,CA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Bromo Cresol Green</td>
			<td>Sigma-Aldrich</td>
			<td>45ZW10</td>
			<td></td>
		</tr>
		<tr>
			<td>Bromo Thymol Blue</td>
			<td>Sigma</td>
			<td>76-59-5</td>
			<td></td>
		</tr>
		<tr>
			<td>ElectraCOOL Advanced thermoelectric cool plate</td>
			<td>Pollock industries, White River, VT, USA</td>
			<td>TCP 50</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Beantown Chemical, 9 Sagamore Park Road 
			Hudson, NH 03051</td>
			<td>64-17-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Gadolinium Oxysulfide Europium doped (Gd2O2S:Eu) particles-~8.0 &#181;m</td>
			<td>Phosphor Technologies Inc., Stevenage, England</td>
			<td>UKL63/N-R1</td>
			<td></td>
		</tr>
		<tr>
			<td>LabVIEW</td>
			<td>National Instruments, Austin, TX</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Motorized Linear Vertical Stage Model (for Z axis)</td>
			<td>Motion Control, Smithtown, NY, USA</td>
			<td>AT10-60</td>
			<td></td>
		</tr>
		<tr>
			<td>National instruments c-DAQ 9171</td>
			<td>National Instruments, Austin, TX</td>
			<td>NI cDAQ&#8482;-9171</td>
			<td></td>
		</tr>
		<tr>
			<td>One piece acrylic light guide</td>
			<td>Produced in Hilltop Technology Laboratory, 51 Parker, Irvine,CA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>pH 4 buffer</td>
			<td>VWR BDH Chemicals</td>
			<td>BDH5024</td>
			<td></td>
		</tr>
		<tr>
			<td>pH 8 buffer</td>
			<td>VWR BDH Chemicals</td>
			<td>BDH5060</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffer Solution</td>
			<td>MP Biomedicals, Irvine, CA. USA</td>
			<td>2810305</td>
			<td></td>
		</tr>
		<tr>
			<td>Photo multiplier tubes Model P25PC-16</td>
			<td>SensTech, Surrey, UK</td>
			<td>Model P25PC-16</td>
			<td></td>
		</tr>
		<tr>
			<td>Staphylococcus aureus subsp. aureus Rosenbach</td>
			<td>American Type Culture Collection (ATCC), Manassas, VA</td>
			<td>ATCC 25923</td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptic Soy Agar</td>
			<td>Teknova, Hollister, CA, USA</td>
			<td>&#160;T0520</td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptic Soy Broth</td>
			<td>EMD Millipore, Burlington, MA, USA</td>
			<td>1005255000</td>
			<td></td>
		</tr>
		<tr>
			<td>X-ray source-iMOXS</td>
			<td>Institute for Scientific Instruments GmbH, Berlin, Germany</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>X,Y motorized stage-30 cm x 15 cm x 6 cm travel</td>
			<td>Thorlabs Inc., Newton, NJ, USA</td>
			<td>LTS300 and LTS150</td>
			<td></td>
		</tr>
	</tbody>
</table>

high spatial resolution chemical imaging of implant-associated infections with x-ray excited luminescence chemical imaging through tissue

Microbial infections associated with implantable medical devices are a major concern in fracture fixation failure. Early diagnosis of such infection will allow successful eradication with antibiotics without an extra cost for a second surgery. Herein, we describe XELCI as a technique with high X-ray resolution, implant specificity, and chemical sensitivity to noninvasively image chemical concentrations near the surface of implanted medical devices. The devices are coated with chemically reporting surfaces. This chemically responsive surface consists of two layers coated on an implantable medical device; a pH-sensitive layer (bromothymol blue or bromocresol green incorporated hydrogel) which is coated over a red-light emitting scintillator (Gd2O2S: Eu) layer for monitoring. A focused X-ray beam irradiates a spot on the implant, and the red light generated by the scintillator (with 620 nm and 700 nm peaks) is transmitted through the sensing layer which alters the spectral ratio depending on the pH. An image is generated by scanning the X-ray beam across the implant and measuring the spectral ratio of light passing through the tissue point-by-point. We used this imaging technique for monitoring implant-associated infections previously on the bone surface of the femur with a modified implantable plate sensor. Now we are studying pH changes that occur from tibial intramedullary rod infections. Two different types of intramedullary rod designs are used in pre-pilot rabbit studies, and we learned that the XELCI technique could be used to monitor any chemical changes that occur not only on the bone surface but also inside the bone. Thus, this enables noninvasive, high spatial resolution, low background local pH imaging to study implant-associated infection biochemistry.

As a preliminary study, we imaged the intramedullary rod sensor in a reamed tibia of a rabbit cadaver14. The sensor has three distinct regions: the reference region, pH 8 region (basic pH), and pH 4 region (acidic pH). The reference region is the scintillator (Gd2O2S:Eu) particle incorporated in roughened epoxy film. The distinctive acidic and basic pH regions represent infected and non-infected situations inside the intramedullary canal (Figure 6A</stron...

Watch this Scientific Journal Video about High Spatial Resolution Chemical Imaging of Implant-Associated Infections with X-ray Excited Luminescence Chemical Imaging Through Tissue at JoVE.com

High Spatial Resolution Chemical Imaging of Implant-Associated Infections with X-ray Excited Luminescence Chemical Imaging Through Tissue

Here, we present a protocol for high-resolution optical detection of chemical information around implanted medical devices with X-ray excited luminescence chemical imaging (XELCI). This novel imaging technique is developed in our lab which enables studying implant-associated infection biochemistry.

Microbial infections associated with implantable medical devices are a major concern in fracture fixation failure. Early diagnosis of such infection will ...

high-spatial-resolution-chemical-imaging-implant-associated

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JoVE Journal

Chemistry

1.2K Views.  Clemson University. Here, we present a protocol for high-resolution optical detection of chemical information around implanted medical devices with X-ray excited luminescence chemical imaging (XELCI). This novel imaging technique is developed in our lab which enables studying implant-associated infection biochemistry. 

Video: High Spatial Resolution Chemical Imaging of Implant-Associated Infections with X-ray Excited Luminescence Chemical Imaging Through Tissue

Free Radicals in Chemical Biology: from Chemical Behavior to Biomarker Development

The involvement of free radicals in life sciences has constantly increased with time and has been connected to several physiological and pathological processes. This subject embraces diverse scientific areas, spanning from physical, biological and bioorganic chemistry to biology and medicine, with applications to the amelioration of quality of life, health and aging. Multidisciplinary skills are required for the full investigation of the many facets of radical processes in the biological environment and chemical knowledge plays a crucial role in unveiling basic processes and mechanisms. We developed a chemical biology approach able to connect free radical chemical reactivity with biological processes, providing information on the mechanistic pathways and products. The core of this approach is the design of biomimetic models to study biomolecule behavior (lipids, nucleic acids and proteins) in aqueous systems, obtaining insights of the reaction pathways as well as building up molecular libraries of the free radical reaction products. This context can be successfully used for biomarker discovery and examples are provided with two classes of compounds: mono-trans isomers of cholesteryl esters, which are synthesized and used as references for detection in human plasma, and purine 5',8-cyclo-2'-deoxyribonucleosides, prepared and used as reference in the protocol for detection of such lesions in DNA samples, after ionizing radiations or obtained from different health conditions.

Radical-based biomimetic chemistry has been applied to building-up libraries necessary for biomarker development.

The involvement of free radicals in life sciences has constantly increased with time and has been connected to several physiological and pathological ...

Confocal Imaging of Confined Quiescent and Flowing Colloid-polymer Mixtures

The behavior of confined colloidal suspensions with attractive interparticle interactions is critical to the rational design of materials for directed assembly1-3, drug delivery4, improved hydrocarbon recovery5-7, and flowable electrodes for energy storage8. Suspensions containing fluorescent colloids and non-adsorbing polymers are appealing model systems, as the ratio of the polymer radius of gyration to the particle radius&#160;and concentration of polymer control the range and strength of the interparticle attraction, respectively. By tuning the polymer properties and the volume fraction of the colloids, colloid fluids, fluids of clusters, gels, crystals, and glasses can be obtained9.&#160;Confocal microscopy, a variant of fluorescence microscopy, allows an optically transparent and fluorescent sample to be imaged with high spatial and temporal resolution in three dimensions. In this technique, a small pinhole or slit blocks the emitted fluorescent light from regions of the sample that are outside the focal volume of the microscope optical system. As a result, only a thin section of the sample in the focal plane is imaged. This technique is particularly well suited to probe the structure and dynamics in dense colloidal suspensions at the single-particle scale: the particles are large enough to be resolved using visible light and diffuse slowly enough to be captured at typical scan speeds of commercial confocal systems10. Improvements in scan speeds and analysis algorithms have also enabled quantitative confocal imaging of flowing suspensions11-16,37.&#160;In this paper, we demonstrate confocal microscopy experiments to probe the confined phase behavior and flow properties of colloid-polymer mixtures. We first prepare colloid-polymer mixtures that are density- and refractive-index matched. Next, we report a standard protocol for imaging quiescent dense colloid-polymer mixtures under varying confinement in thin wedge-shaped cells. Finally, we demonstrate a protocol for imaging colloid-polymer mixtures during microchannel flow.

Confocal microscopy is used to image quiescent and flowing colloid-polymer mixtures, which are studied as model systems for attractive suspensions. Image analysis algorithms are used to calculate structural and dynamic metrics for the colloidal particles that measure changes due to geometric confinement.

The behavior of confined colloidal suspensions with attractive interparticle interactions is critical to the rational design of materials for directed ...

Preparing Adherent Cells for X-ray Fluorescence Imaging by Chemical Fixation

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over large or small sample areas. It has been applied in many areas of science, including materials science, geoscience, studying works of cultural heritage, and in chemical biology. In the case of chemical biology, for example, visualizing the metal distributions within cells allows us to study both naturally-occurring metal ions in the cells, as well as exogenously-introduced metals such as drugs and nanoparticles. Due to the fully hydrated nature of nearly all biological samples, cryo-fixation followed by imaging under cryogenic temperature represents the ideal imaging modality currently available. However, under the circumstances that such a combination is not easily accessible or practical, aldehyde based chemical fixation remains useful and sometimes inevitable. This article describes in as much detail as possible in the preparation of adherent mammalian cells by chemical fixation for X-ray fluorescent imaging.

Here, we present a protocol on how to determine the quantity and distribution of metals in a sample using synchrotron X-ray fluorescence. We focus on adherent cells, and describe the chemical fixation method to prepare this sample. We then describe how to mount and image the sample using synchrotron X-rays.

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over ...

Chemical Gardens as Flow-through Reactors Simulating Natural Hydrothermal Systems

Here we report experimental simulations of hydrothermal chimney growth using injection chemical garden methods. The versatility of this type of experiment allows for testing of various proposed ocean / hydrothermal fluid chemistries that could have driven reactions toward the origin of life in environments on the early Earth, early Mars, or even other worlds such as the icy moons of the outer planets. We show experiments that include growth of chemical garden structures under anoxic conditions simulating the early Earth, inclusion of trace components of phosphates / organics in the injection solution to incorporate them into the structure, a switch of the injection solution to introduce a secondary precipitating anion, and the measurement of membrane potentials generated by chemical gardens. Using this method, self-assembling chemical garden structures were formed that mimic the natural chimneys precipitated at submarine hydrothermal springs, and these precipitates can be used successfully as flow-through reactors by feeding through multiple successive &#8220;hydrothermal&#8221; injections.

We describe chemical garden formation via injection experiments that allow for laboratory simulations of natural chemical garden systems that form at submarine hydrothermal vents.

Here we report experimental simulations of hydrothermal chimney growth using injection chemical garden methods. The versatility of this type of experiment ...

Quantifying X-Ray Fluorescence Data Using MAPS

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical composition and elemental distribution within a material. Synchrotron-based XRF has become an integral characterization technique for a variety of research topics, particularly due to its non-destructive nature and its high sensitivity. Today, synchrotrons can acquire fluorescence data at spatial resolutions well below a micron, allowing for the evaluation of compositional variations at the nanoscale. Through proper quantification, it is then possible to obtain an in-depth, high-resolution understanding of elemental segregation, stoichiometric relationships, and clustering behavior.
This article explains how to use the MAPS fitting software developed by Argonne National Laboratory for the quantification of full 2-D XRF maps. We use as an example results from a Cu(In,Ga)Se2 solar cell, taken at the Advanced Photon Source beamline 2-ID-D at Argonne National Laboratory. We show the standard procedure for fitting raw data, demonstrate how to evaluate the quality of a fit and present the typical outputs generated by the program. In addition, we discuss in this manuscript certain software limitations and offer suggestions for how to further correct the data to be numerically accurate and representative of spatially resolved, elemental concentrations.

Here, we demonstrate the use of the X-ray fluorescence fitting software, MAPS, created by Argonne National Laboratory for the quantification of fluorescence microscopy data. The quantified data that results is useful for understanding the elemental distribution and stoichiometric ratios within a sample of interest.

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical ...

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 &#181;m grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes in detail how to fabricate and operate microfluidic devices for X-ray diffraction data collection at room temperature. Additionally, it describes how to monitor protein crystallization by dynamic light scattering and how to process and analyze obtained diffraction data.

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The ...

Elemental-sensitive Detection of the Chemistry in Batteries through Soft X-ray Absorption Spectroscopy and Resonant Inelastic X-ray Scattering

Energy storage has become more and more a limiting factor of today's sustainable energy applications, including electric vehicles and green electric grid based on volatile solar and wind sources. The pressing demand of developing high-performance electrochemical energy storage solutions, i.e., batteries, relies on both fundamental understanding and practical developments from both the academy and industry. The formidable challenge of developing successful battery technology stems from the different requirements for different energy-storage applications. Energy density, power, stability, safety, and cost parameters all have to be balanced in batteries to meet the requirements of different applications. Therefore, multiple battery technologies based on different materials and mechanisms need to be developed and optimized. Incisive tools that could directly probe the chemical reactions in various battery materials are becoming critical to advance the field beyond its conventional trial-and-error approach. Here, we present detailed protocols for soft X-ray absorption spectroscopy (sXAS), soft X-ray emission spectroscopy (sXES), and resonant inelastic X-ray scattering (RIXS) experiments, which are inherently elemental-sensitive probes of the transition-metal 3d and anion 2p states in battery compounds. We provide the details on the experimental techniques and demonstrations revealing the key chemical states in battery materials through these soft X-ray spectroscopy techniques.

Here, we present a protocol for typical experiments of soft X-ray absorption spectroscopy (sXAS) and resonant inelastic X-ray scattering (RIXS) with applications in battery material studies.

Energy storage has become more and more a limiting factor of today's sustainable energy applications, including electric vehicles and green electric grid ...

Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles

The size, size distribution and stability of colloidal nanoparticles are greatly affected by the presence of capping ligands. Despite the key contribution of capping ligands during the synthesis reaction, their role in regulating the nucleation and growth rates of colloidal nanoparticles is not well understood. In this work, we demonstrate a mechanistic investigation of the role of trioctylphosphine (TOP) in Pd nanoparticles in different solvents (toluene and pyridine) using in situ SAXS and ligand-based kinetic modeling. Our results under different synthetic conditions reveal the overlap of nucleation and growth of Pd nanoparticles during the reaction, which contradicts the LaMer-type nucleation and growth model. The model accounts for the kinetics of Pd-TOP binding for both, the precursor and the particle surface, which is essential to capture the size evolution as well as the concentration of particles in situ. In addition, we illustrate the predictive power of our ligand-based model through designing the synthetic conditions to obtain nanoparticles with desired sizes. The proposed methodology can be applied to other synthesis systems and therefore serves as an effective strategy for predictive synthesis of colloidal nanoparticles.

The main goal of this work is to elucidate the role of capping agents in regulating the size of palladium nanoparticles by combining in situ small angle x-ray scattering (SAXS) and ligand-based kinetic modeling.

The size, size distribution and stability of colloidal nanoparticles are greatly affected by the presence of capping ligands. Despite the key contribution ...

High Resolution Physical Characterization of Single Metallic Nanoparticles

Individual molecules can be detected and characterized by measuring the degree by which they reduce the ionic current flowing through a single nanometer-scale pore. The signal is characteristic of the molecule&#39;s physicochemical properties and its interactions with the pore. We demonstrate that the nanopore formed by the bacterial protein exotoxin Staphylococcus aureus alpha hemolysin (&#945;HL) can detect polyoxometalates (POMs, anionic metal oxygen clusters), at the single molecule limit. Moreover, multiple degradation products of 12-phosphotungstic acid POM (PTA, H3PW12O40) in solution are simultaneously measured. The single molecule sensitivity of the nanopore method allows for POMs to be characterized at significantly lower concentrations than required for nuclear magnetic resonance (NMR) spectroscopy. This technique could serve as a new tool for chemists to study the molecular properties of polyoxometalates or other metallic clusters, to better understand POM synthetic processes, and possibly improve their yield. Hypothetically, the location of a given atom, or the rotation of a fragment in the molecule, and the metal oxidation state could be investigated with this method. In addition, this new technique has the advantage of allowing the real-time monitoring of molecules in solution.&#160;

Here, we present a protocol to detect discrete metal oxygen clusters, polyoxometalates (POMs), at the single molecule limit using a biological nanopore-based electronic platform. The method provides a complementary approach to traditional analytical chemistry tools used in the study of these molecules.

Individual molecules can be detected and characterized by measuring the degree by which they reduce the ionic current flowing through a single ...

Luminescence Lifetime Imaging of O2 with a Frequency-Domain-Based Camera System

We describe a method to image dissolved oxygen (O2), in 2D at high spatial (&#60; 50-100 &#181;m) and temporal (&#60; 10 s) resolution. The method employs O2 sensitive luminescent sensor foils (planar optodes) in combination with a specialized camera system for imaging luminescence lifetime in the frequency-domain. Planar optodes are prepared by dissolving the O2-sensitive indicator dye in a polymer and spreading the mixture on a solid support in a defined thickness via knife coating. After evaporation of the solvent, the planar optode is placed in close contact with the sample of interest - here demonstrated with the roots of the aquatic plant Littorella uniflora. The O2 concentration-dependent change in the luminescence lifetime of the indicator dye within the planar optode is imaged via the backside of the transparent carrier foil and aquarium wall using a special camera. This camera measures the luminescence lifetime (&#181;s) via a shift in phase angle between a modulated excitation signal and emission signal. This method is superior to luminescence intensity imaging methods, as the signal is independent of the dye concentration or intensity of the excitation source, and solely relies on the luminescence decay time, which is an intrinsically referenced parameter. Consequently, an additional reference dye or other means of referencing are not needed. We demonstrate the use of the system for macroscopic O2 imaging of plant rhizospheres, but the camera system can also easily be coupled to a microscope.

Luminescence Lifetime Imaging of O2 with a Frequency-Domain-Based Camera System

We describe the use of a novel, frequency-domain luminescence lifetime camera for mapping 2D O2 distributions with optical sensor foils. The camera system and image analysis procedures are described along with the preparation, calibration and application of sensor foils for visualizing the O2 microenvironment in the rhizosphere of aquatic plants.

We describe a method to image dissolved oxygen (O2), in 2D at high spatial (&#60; 50-100 &#181;m) and temporal (&#60; 10 s) resolution. The method employs ...