Thursday, July 2, 2015

Variable Bandwidth Monochromators: A Useful tool for Quantifying Fluorescent Probes in Produced Effluent Water

Produced effluent water is one of the primary waste products of the process of separating oil, gas and water and is typically a mixture of formation and injection process water containing oil, salts, chemicals, solids and trace metals. Stringent environmental regulations require producers to monitor oil content in water streams from oil production and refining. To further reduce the level of crude oil released in produced water streams, more advanced methods are necessary to accurately detect minute traces of oil in purified samples; down to parts per million (ppm) or parts per billion (ppb) levels.

Several reference methods have historically been used by the industry to measure oil in produced water. These include infrared absorption, gravimetric, and gas chromatography and flame ionization detection (GC-FID) methods. However, none have been universally adopted, and all are subject to limitations. Newer methods, which incorporate a fluorescent probe, overcome the limitations of each of the previously listed methods, and also deliver a high level of sensitivity. Fluorescent probes can also be used to monitor other pollutants, provided that the dye molecule has a high partitioning coefficient into the contaminant.

BioTek’s new Synergy™ Neo2 Multi-Mode Reader has a monochromator-based detection system that can scan and record excitation and emission spectra for fluorescent probes used in produced effluent water, such as those shown above for the unknown sample 201. The spectra provide the basis for optimizing wavelength and bandwidth selection, using the excitation and emission variable bandwidth monochromators in Synergy Neo2. With Gen5 Software, multiple parameters can be tested in the same experiment, setting excitation and emission values at the determined spectral peaks, or off the peak in order to lower potential crosstalk.

The sensitivity of each parameter combination can then be assessed by examining calculated signal to noise and limit of detection (LOD) values.

The results of the complete set of reads confirm that the flexibility of the variable bandwidth monochromators on the Synergy Neo2 provide the most ideal parameters to easily detect trace crude oil levels and other potential pollutants in effluent water streams. We invite you to learn more about this application, as well as the Synergy Neo2, by following the link to read the entire application note.

By: BioTek Instruments, Brad Larson, Principal Scientist

Tuesday, June 23, 2015

Top 10 Tips for Cellular Microscopy: Part 2

6. Proper Focusing

Autofocusing is the most popular method used in automated imaging. A label-free assay requires brightfield or phase contrast imaging channels to be used for image focus - unlabeled cells provide limited contrast from background, so proper illumination of the sample is critical. It can be helpful to initially use manual imaging to find the z-height where samples are appropriately focused. Incorporation of this value into Vessel z-height should be added to vessel definition specifications in software so that the proper z-height is used to begin the auto-focus process, which can minimize focus time.

With fluorescence imaging, auto-focusing may be accomplished using the signal from an included fluorescent label. While this works to improve the ease of focus in many situations, certain caveats still exist: A fluorophore with a strong signal allows for the proper focal plane to be found easily, minimizing time spent focusing on each sample. Conversely, a fluorophore with a weak signal, or high background signal, lowers contrast within the image and can cause images to be out of focus. Localization of the fluorophore to the specific area of the cell also needs to be taken into account when using objectives with high numerical aperture and limited depth of field. Use of a nuclear stain will lead to accurate focusing on the nucleus of a cell, but when using. a second channel to image fluorescence emanating from a fluorophore localized to the plasma membrane, the image may be improperly focused, as the two cellular compartments exist on slightly different focal planes. A fixed z-offset can accommodate this difference and can easily correct for the disparity.

Finally, fixed-focusing can be used in lieu of auto-focus, when a high degree of confidence exists that samples exist at the same focal plane across multiple wells or fields of view. Fixed-focusing can also be used when a cursory view of the state of an experiment or process is necessary. By eliminating the auto-focus procedure, imaging is immediately carried out on all samples, in the fastest possible processing time.

7. Establish Optimal Image Acquisition (Exposure) Settings

Appropriate image acquisition settings are critical for obtaining meaningful, quantifiable data and images suitable for use in publication. These settings typically include excitation light intensity, camera gain and integration time. Qualitative microscopy uses image acquisition setting, that provide the best looking image. Quantitative digital microscopy adjusts exposure parameters such that the entire bit depth of the camera is used as much as possible.

When using a fixed exposure for all wells included in an experimental imaging step, use positive and negative controls, if possible, to establish exposure settings. This will help avoid pixel saturation, while maintaining an exposure that will also accurately quantify changes in fluorescence amongst test samples. Saturated pixels cannot be accurately quantified causing the dataset to be truncated at the maximum end of the dynamic range. Conversely, parameters that are set too low, often used to hide “background” cellular fluorescence, truncates the data at the minimum end of the dynamic range and again skews quantitative measurements. Manual imaging can also be used for this function, with the final parameters then being transferred to the automated imaging step. If a change in fluorescence is expected between test wells, or between sample and control wells, the auto-exposure function should not be used, as the imager will attempt to compensate for high and low signals by adjusting the parameters accordingly. This will result in a normalization of the data, and elimination of the expected assay window. Auto-exposure is useful to start the optimization process, if single samples are being analyzed, or if a comparison between actual signal values is not part of the analysis criteria.

8. Kinetic Imaging

Kinetic imaging to track cellular changes in real time can yield important nuances that might otherwise be missed in a single end point image. An additional benefit to kinetic imaging is the ability to create a movie from the images captured over time, allowing for visualization of an expected change, in addition to numerical quantification. As with all imaging, however, certain guidelines must be followed to guarantee the best possible images are captured and data obtained.

Fixed exposure is recommended for the kinetic experimental procedure. Most likely there will be a desire to quantify the change to the sample that will occur over the incubation period, and fixed exposure will prevent data normalization over the kinetic time period. If a reduction in signal is expected, use a positive control for parameter optimization. If an increase is expected, use a negative control. Take care, however, to not choose a setting too low which will not allow the expected change in signal to fall within the linear range of the assay. Fluorophores should also be stable, with low susceptibility to photo-bleaching during the entire length of the imaging procedure.

9. Pixel Shift

Pixel shift occurs when a filter in an imaging path diverts the light rays, resulting in a shift of the image detected on a high-resolution CCD camera. Typically this is caused by emission filters not being of uniform thickness, referred to as filter wedge. This shift becomes problematic when two or more images of the same object are acquired using different filter sets and then overlaid in order to simultaneously view fluorescence from multiple fluorophores. Images produced by different fluorophores will not be accurately correlated or combined because each image is shifted by a differently according to the wedge angles found in each filter set.Because even the most expensive objectives and filters will have some aberration, calibration routines are used to correct for this phenomenon. With automated digital microscopes, this is often done during the LED and objective calibration steps. Using brightfield as a reference of illumination, each LED and objective combination is tested for pixel shift by determination of the center of an aperture. The calculated pixel shift for each is then used to offset images such that overlays are in their proper location. Individual colors from multi-color images can also be repositioned after imaging using a channel shift tool in some digital microscopy software. For example, a live specimen moving during separate fluorescent color imaging steps can result in slight misalignment of the different colors with overlaid images. Because different color channels are imaged in sequence there is a short temporal interval between images that can capture specimen movement. The channel shift tool allows the researcher to reposition the channel in order to correct for the movement.

10. Establish Favorable Environmental Conditions

Long term kinetic live cell imaging typically requires some control of environmental conditions to maintain sample viability. Temperature is a main consideration. While most mammalian cells grow at 37 °C, if bacterial or yeast cells are used, higher or lower temperatures may be required. Manual pre-setting, or inclusion of a temperature control step into the procedure, can ensure that proper temperatures are maintained while imaging is performed. Atmospheric control can also be critical. For example, maintenance of 5% CO2/95% air within the imaging chamber provides an appropriate atmosphere for mammalian cells. When combined, provision of the correct temperature and atmospheric conditions can allow live cell imaging to take place without sacrificing sample integrity over long kinetic reads.

By: BioTek Instruments

Tuesday, June 16, 2015

Top 10 Tips for Cellular Microscopy: Part 1

1. Sample Preparation

Sample preparation is critical to ensure high quality images. Cells should be at an adequate density when harvested from the tissue culture flask, and removed with an appropriate dissociation solution to retain essential cellular function. Use aseptic technique to prevent contamination during the experiment and avoid unnecessary introduction of foreign particles or cellular debris that can negatively impact image quality.

For live cell assays, fluorescent probes need to be cell membrane permeable to assess structure and function within the cell. Optimize concentrations and incubation times prior to performing the actual assay to maintain cell viability while still ensuring sufficient fluorescence. Be aware of potential background fluorescence - it may be necessary to incorporate wash steps before imaging. Together, these will help to provide images of live cells with good signal to background ratios.

For fixed cell assays such as immunofluorescence, always use a proven fixing/permeabilizing/staining protocol, including, addition of a blocking agent to prevent non-specific binding, and optimization of antibody concentrations when necessary.

2. Sample Vessel Considerations

The bottom thickness of sample vessels used for microscopy is important, since inverted microscopes view samples through this thickness. Different vessels have different bottom thicknesses. Some common vessel bottom thicknesses include:
  • microscope slide cover glass: 0.17 mm
  • common plastic microplates: 0.5 mm
  • low density microplates: 1.0 mm
Newer microplates, developed specifically for imaging, have bottom thicknesses closer to that of a cover glass. When imaging with lower numerical aperture objectives (< 0.7), vessel bottom thickness is not a great concern. However when air objectives with high numerical apertures (0.8 or greater) are used, variations of just a few micrometers in vessel thickness can cause image degradation. Aberrations get worse as the vessel thickness increases. A correction collar is used to compensate for these errors. The collar allows for adjustment of the positioning of the central lens group within the objective and insures proper image focusing no matter what type of vessel is used.

3. Cell Number Optimization

Typically cell-based assays are more robust when there are more cells. Cellular imaging is a bit trickier; plating too many cells can cause cells to grow on top of each other, confusing proper segmentation of cells for cell counting or other assessments. Plating too few cells can be statistically insignificant and skew cell sub-population analysis. Post-plating and post-treatment incubation times should also be factored into cell number determination, as cell propagation can continue during the preparation and execution of the experiment.

4. Cell Type

A wide variety of cell types can be used for cellular imaging, including immortalized cell lines, primary cells, and stem cells. Most cell types used in microscopy applications are adherent in nature; with the right treatment, the cells will adhere and form a two-dimensional (2D) layer of cells across the bottom of the well. 2D is the most straightforward format for imaging, as the cells are in a single plane which can be found using the auto-focus capability of the imager.

Suspension cells, such as erythrocytes and leukocytes, can also be imaged. These cell types lack the ability to adhere to a surface and require additional manipulation to restrict them to a single focal plane at the surface of the vessel used for microscopy. Suspension cells can be transferred onto a microscope slide with coverslip or hemocytometer with cover glass which restricts the cells in the axial direction and provides better image clarity. With microplates, a centrifugation step can also be used to induce cells to the bottom of the well.

More complicated biology, such as tissues and three-dimensional (3D) cellular structures, have also been incorporated into image-based experimental processes. The difference in size and shape compared to individual 2D-plated cells, make more advanced imaging procedures necessary. Tissue samples can often be much larger than the field of view provided by the microscope objective, particularly if high resolution is desired with high numerical aperture objectives. An image montage procedure captures numerous images across the entire tissue which can then be stitched together into a single composite image which can then be used for analysis. 3D cellular structures contain hundreds to thousands of cells which extend not only in the x- and y-axes, but also in the z-axis. Capturing a z-stacked set of images across multiple z-planes, coupled with z-projection image processing allows for a composite image with better focus than any one of the individual z-stack images. This z-projected composite image can increase the accuracy of any subsequent analysis.

5. Fluorophores and Imaging Filter Sets

It’s essential to use the best fluorophore for successful imaging. Excitation and emission spectra of the fluorescent probe or protein should be matched with LED light sources, excitation and emission filters, and dichroic mirrors available to assure satisfactory fluorescent signal. The fluorophore's Stokes shift is an important variable to consider as narrow Stokes shift can lead to excessive background fluorescence and poor signal to background. Additional optimization is necessary if multiple fluorophores are used together in a multiplexed format. Molecular spectra tend to be broad and overlap in both excitation and emission spectra can occur, resulting in bleed-through of one fluorophore into the fluorescent channel of another. This is particularly important should both fluorophores be colocalized in the same area within a cell.

By: BioTek Instruments

Tuesday, June 9, 2015

Think Possible

It is a well known fact that many modern drugs have been recalled due to cardiotoxicity. There are a number of models for testing drug cardiotoxicity, and the development of new cell lines has shown potential to enhance these models. One of these cell lines, as recently reported in the June 3, 2015 web edition of Point to Point, the news and information bulletin from SLAS, is the Axiogenesis "Cor.4U human cardiomyocyte product derived from induced pluripotent stem (iPS) cells". This cell line is designed for use "in applications from single cell analysis to high-throughput screening (HTS) of pharmaceutical compounds". Importantly, according to the Axiogenesis news thread, the Cor.4U cell line will be applied to cardiac safety assessment as part of the company's participation in the "The Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative, led by the US Food & Drug Administration (FDA), Safety Pharmacology Society (SPS), Cardiac Safety Research Consortium (CSRC), and the Health & Environmental Sciences Institute (HESI)". The aim of this global initiative is "to improve current regulatory guidance by introducing predictive technologies, including human stem cell-derived ventricular cardiomyocytes, into preclinical safety assessment".

Axiogenesis recently presented a poster titled Analysis of Mitochondrial Function Using Human iPSC-Derived Cardiomyocytes on The Seahorse XF96 Analyzer at the Society of Toxicology (SOT) 54th Annual Meeting, 22-26 March 2015, San Diego CA USA. At the same SOT conference one of our collaborators, Luxcel Biosciences, presented collateral created with us from a poster presentation at SLAS 2015 Optimization of a Multi-Mode Detection Model for Measuring Real-time Cellular Respiration and Mitochondrial Function using Fluorophoric Biosensors.

The Luxcel probes used by BioTek for the SLAS poster and Application Note content measure cellular metabolism in microplate readers, and are an alternative approach to the Seashorse XF96 Analyzer, a high-end closed system, used by Axiogenesis in their SOT poster presentation. Not missing a beat, Luxcel joined up with Axiogenesis and recently demonstrated the merits of the Luxcel approach via data now released in the Application Note Mitochondrial Toxicity Assay in Stem Cell Derived Cor.4U® Cardiomyocytes. Among other conclusions of the Luxcel/Axiogenesis work, the "data illustrate the potential of stem cell derived cardiomyocytes in screening compounds for potential cardiotoxicity using microtitre plate based measurement of both mitochondrial function and glycolytic flux using a human model (Cor.4U®) and the MitoXpress® Xtra - Oxygen Consumption Assay (HS Method) and pH-Xtra® - Glycolysis Assay". An example of their data is shown for the MitoXpress assay below left.

Using HepG2 cells and the Luxcel probes to demonstrate cell metabolic activity in response to compound treatment in a cancer model system, lifetime (┬Ás) data we generated from the BioTek Synergy Neo is shown above right. Similar data for the pH probe is also shown by both Application Notes. The correlation between the Cor.4U cardiomyocytes and the HepG2 cell data would support expansive potential for cell metabolic analysis using the Luxcel probes and a variety of BioTek readers. Think possible!

By: BioTek Instruments, Wendy Goodrich, Applications Scientist

Tuesday, May 26, 2015

3D Printing in Medicine

The first I knew of prosthetics was from the cheesy 70's TV drama "The Six Million Dollar Man," where the fictional astronaut, Steve Austin undergoes state-sanctioned surgery to replace certain body parts that he lost in a terrible spaceship crash with machine-like “bionics”. You can find the Intro to the TV show on YouTube. As the TV title suggests, prosthetics are not cheap (and that’s in 1970 dollars!), albeit those that Mr. Austin had were apparently powered by their own highly efficient little motors which enabled him to come close to emulating Superman. Never did figure out where he had the batteries.

Non-fictional modern prostheses have come a long way from the stereotypical peg legs seen on sailors. They can even come with small electric motors to allow patients to use their prosthesis in a similar fashion to the original limb, just not like Steve Austin! Even without the motors, prostheses are expensive primarily because they need to fit the patient and can’t be mass produced. This is particularly unfortunate for children who can rapidly outgrow their prosthesis.

New developments in 3D printing have appeared to solve this problem, where prostheses can be produced for as little as $5! 3D printing is being investigated for many roles in regenerative medicine, including printing cells to make tissues such as bones, cartilage and skin! There is also the potential to 3D print more complex biological structures such as organs! Stay tuned...

By: BioTek Instruments, Peter Banks Ph.D., Scientific Director

Tuesday, May 5, 2015

Honey Bee Health and the Critical Link to U.S. Agriculture

Most of us are aware of the role honey bees play in the pollination of plants in the United States but what many don’t realize is how critical they are to commercial crop production. While there are several native pollinators in the U.S., the honey bee was introduced to the New World when European settlers arrived. The honey bee proved to be much more prolific and colonies easy to manage as agriculture expanded across the nation. Honey bees have become indispensible for the production of several crops as evident by the complete dependence of the California almond industry on some 1.4 million colonies, representing ~60% of all colonies in the U.S managed for crop production. Commercial production of several other crops including nuts, fruits, berries and vegetables also depend on pollination by honey bees.
Unfortunately, the U.S. has seen a significant decrease in the total number of managed colonies from ~5 million in the 1940s to 2.5 million today! Along the way the loss and replacement of approximately 10 million bee hives came at a replacement cost of ~ $2 billion. The trend has also been seen on a global scale coinciding with an increased demand for pollination services for commercial operations.

While the disappearance of colonies is well documented, the problem remains a mystery designated Colony Collapse Disorder (CCD). Symptoms of the syndrome include the absence of adult bees or dead bee bodies in the presence of a live queen and brood as well as honey in the hive. The decline in the U.S. has been associated with the introduction of several new pathogens and pests in the 1980s and carriers of viral agents such as Varroa and tracheal mites during the 1990s. However, no single scientific cause has been verified to date leading to CCD. Research suggests rather, that a combination of environmental and pathological stresses can lead to CCD.

Current research has defined the four general categories mentioned above as probable causes contributing to CCD: 1) Pathogens, 2) Parasites, 3) Management stressors and 4) Environmental stressors. Field surveys and laboratory research have supported a number of potential causes yet none have held up to rigorous examination leading to a definitive “cause” of CCD.

One such area of research investigates the affect of the gradual speciation shift in favor of the microsporidia pathogen Nosema ceranae over N. apis via a survey of bee hives across the U.S. Data suggest that infection immunosuppresses honey bees and negatively affects nutrient utilization negatively impacting colony health. Pathogen load via a spore count can be indicative of the health of the colony and generally requires sampling several bees from numerous hives; typically ~ 8-10,000 samples are surveyed over the typical active bee season. Currently the survey relies on manual counting methods similar to blood cell counting using a hemocytometer. BioTek has been working with researchers to provide an automated solution to handle examination of the complex samples of macerated bees. The use of the Cytation 5 at higher magnification (20x) in conjunction with a disposable hemocytometer offers a possible automated solution for determination of spore count (figure 1). Keep tuned for further developments as we continue to work towards validation of this methodology.

Figure 1. Image taken at 20x magnification. Macerated bee sample visualized using phase contrast at 20x magnification. Spores outlined in yellow fit the criteria for intensity, size and circularity while those outlined in red are excluded by non-conformity to the defined circularity criteria

By: BioTek Instruments, Peter J. Brescia Jr., MSc, MBA

Monday, April 27, 2015

The three R’s now spell STEM

It used to be that reading, 'riting and 'rithmetic were the fundamentals of a good education. Now the general consensus is that STEM (science, technology, engineering and math) is the key to success. And boy is it everywhere! Not only are our children exposed to programs at school, they can even attend STEM clubs and camps. For example, some of our awesome BioTek engineers volunteered their time at the 2014-2015 FIRST Tech Robotics Challenge held at the University of Vermont on Pi day (3.14.15). Over 300,000 children competed worldwide for scholarships in this STEM-based competition!

CNN host and writer Fareed Zakaria wrote a recent opinion piece titled "Why America's obsession with STEM education is dangerous". Them's fightin' words Mr. Zakaria! Especially since I’ve been thinking a lot about college lately, for my child that is. And as you may guess, I am one of those parents trying to steer their child towards a STEM major. It’s what I know and mom always knows best, right?

Mr. Zakaria's article got me wondering whether it has to be a left-brain/right-brain world and if you’re a problem-solver, couldn't you be artistic as well? I wouldn't choose the same words as Mr. Zakaria but I understand what he’s trying to say, that a focus on STEM doesn’t guarantee success but rather, one needs the ability to think intelligently and creatively. After all, this is what fosters entrepreneurship and innovation.

By: BioTek Instruments, Ellaine Abueg Ph.D., Product Manager, Specialist