Size exclusion chromatography for screening yeastolate used in cell culture media

Yeastolate is often used as a media supplement in industrial mammalian cell culture or as a major media component for microbial fermentations. Yeastolate variability can significantly affect process performance, but analysis is technically challenging because of its compositional complexity. However, what may be adequate for manufacturing purposes is a fast, inexpensive screening method to identify molecular variance and provide sufficient information for quality control purposes, without characterizing all the molecular components. Here we used Size Exclusion Chromatography (SEC) and chemometrics as a relatively fast screening method for identifying lot-to-lot variance (with Principal Component Analysis, PCA) and investigated if Partial Least Squares, PLS, predictive models which correlated SEC data with process titer could be obtained. SEC provided a relatively fast measure of gross molecular size hydrolysate variability with minimal sample preparation and relatively simple data analysis. The sample set comprised of 18 samples from 12 unique source lots of an ultra-filtered yeastolate (10 kDa molecular weight cut-off) used in a mammalian cell culture process. SEC showed significant lot-to-lot variation, at 214 and 280 nm detection, with the most significant variation, that correlated with process performance, occurring at a retention time of ∼6 min. PCA and PLS regression correlation models provided fast identification of yeastolate variance and its process impact. The primary drawback is the limited column lifetime (<300 injections) caused by the complex nature of yeastolate and the presence of zinc. This limited long term reproducibility because these age-related, non-linear changes in chromatogram peak positions and shapes were very significant.

Analyzing protein conjugation reactions for antibody-drug conjugate synthesis using polarized excitation emission matrix spectroscopy

Antibody-drug conjugates (ADCs) are promising anticancer therapeutics, which offer important advantages compared to more classical therapies. There are a variety of ADC critical quality attributes (CQAs) such as the protein structure, aggregation, and drug-to-antibody ratio (DAR), which all impact on potency, stability, and toxicity. Production processes can destabilize antibodies via a variety of physical and chemical stresses, and or by increased aggregation after conjugation of hydrophobic drugs. Thus, a proper control strategy for handling, production, and storage is necessary to maintain CQA levels, which requires the use of in-process quality measurements to first identify, then understand, and control the variables which adversely affect ADC CQAs during manufacturing. Here, we show how polarized excitation emission matrix (pEEM) spectroscopy, a sensitive, nondestructive, and potentially fast technique, can be used for rapidly assessing aggregation and DAR in a single measurement. pEEM provides several sources of information for protein analysis: Rayleigh scatter for identifying aggregate/particle formation and fluorescence emission to assess chemical and structural changes induced by attachment of a linker and/or a small molecule drug payload. Here, we used a nontoxic ADC mimic (monoclonal antibody with linker molecule) to demonstrate efficacy of the measurement method. Emission changes caused via light absorption by the attached linker, allowed us to predict DAR with good accuracy using fluorescence signal from the final purified products (6% relative error of prediction [REP]) and also from unpurified alkylation intermediates (11% REP). pEEM changes could also be correlated with size (hydrodynamic radius, R_h ) and aggregate content parameters obtained from dynamic light scattering and size exclusion chromatography (SEC). For the starting material and purified product samples, pEEM correlated better with R_h (R²  = 0.99, 6% REP) than SEC determined aggregate content (18% REP). Combining both fluorescence and light scatter signals also enabled in-process size quantification (6% REP). Overall, combining polarized measurements with EEM and Rayleigh scatter provides a single measurement, multi-attribute test method for ADC manufacturing.

Evaluating the interaction of human serum albumin (HSA) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes in different aqueous environments using anisotropy resolved multi-dimensional emission spectroscopy (ARMES)

Studying the interaction between plasma proteins and liposomes is critical, particularly for their use as drug delivery systems. Here, the efficacy of anisotropy resolved multidimensional emission spectroscopy (ARMES) for investigating the interaction of human serum albumin (HSA) with liposomes was explored and compared to conventional spectroscopic techniques. Dynamic Light Scattering (DLS) and absorbance spectroscopy (with Multivariate Curve Resolution (MCR) modeling) indicated that the highest degree of liposome rupturing, and aggregation occurred in water, with less in ammonium bicarbonate buffer (ABC) and phosphate buffered saline (PBS). Fluorescence emission spectra of HSA-liposome mixtures revealed significant hypsochromic shifts for water and ABC, but much less in PBS, where the data suggests a non-penetrating protein layer was formed. Average fluorescence lifetimes decreased upon liposome interaction in water (6.2→5.2 ns) and ABC buffer (6.3→5.6 ns) but increased slightly for PBS (5.6→5.8 ns). ARMES using polarized Total Synchronous Fluorescence Scan measurements with parallel factor (PARAFAC) analysis resolved intrinsic HSA fluorescence into two components for interactions in water and ABC buffer, but only one component for PBS. These components, in water and ABC buffer, corresponded to two different HSA populations, one blue-shifted and penetrating the liposomes (λ_ex/em = ~ 280/320 nm) and a second, similar to free HSA in solution (λ_ex/em = ~ 282/356 nm). PARAFAC scores for water and ABC buffer suggested that a large proportion of HSA interacted in an end on configuration. ARMES provides a new way for investigating protein-liposome interactions that exploits the full intrinsic emission space of the protein and thus avoids the use of extrinsic labels. The use of multivariate data analysis provided a comprehensive and structured framework to extract a variety of useful information (resolving different fluorescent species, quantifying their signal contribution, and extracting light scatter signals) all of which can be used to discriminate between interaction mechanisms.

Effects of Viscosity and Refractive Index on the Emission and Diffusion Properties of Alexa Fluor 405 Using Fluorescence Correlation and Lifetime Spectroscopies

Fluorescence Correlation Spectroscopy (FCS) studies of the interaction of polymers or proteins in solution are strongly affected by the viscosity and refractive index of the medium, and the effects are likely to be more significant with the use of short wavelength excitation (e.g., 405 nm diode lasers). Failing to account for these issues can lead to incorrect measurement of average size, conformational changes, and dynamic behaviour of polymers and proteins. Steady-state, time-resolved, and FCS measurements of Alexa 405 in glycerol:water mixtures were performed to determine its suitability for FCS measurements with 405 nm excitation. The effects of the refractive index and viscosity on the diffusion coefficient and photophysical parameters (lifetime and relative quantum yield) of the fluorophore were determined. Alexa 405 lifetime decreased from 3.55 ns in water to 3.25 ns in a 50:50 glycerol:water mixture, while its diffusion coefficient dropped from 333 ± 16 to 44 ± 1 µm²s^- 1. Lifetime data collected from micromolar solutions of Alexa 405 did however also suggest that as solvent polarity decreased, aggregates (excimers) were formed as evidenced by the appearance of a rising edge in the decay plots. The interdependence between lifetime, refractive index, and diffusion coefficient could be accurately fitted by a simple polynomial function indicating that the probe is well behaved and predictable in the glycerol:water model system. Overall, Alexa 405 is a most promising and reliable probe for FCS measurement using violet laser diode excitation sources.

Development of a rapid polarized total synchronous fluorescence spectroscopy (pTSFS) method for protein quantification in a model bioreactor broth

Protein quantification during bioprocess monitoring is essential for biopharmaceutical manufacturing and is complicated by the complex chemical composition of the bioreactor broth. Here we present the early-stage development and optimization of a polarized total synchronous fluorescence spectroscopy (pTSFS) method for protein quantification in a hydrolysate-protein model (mimics clarified bioreactor broth samples) using a standard benchtop laboratory fluorometer. We used UV transmitting polarizers to provide wider range pTSFS spectra for screening of the four different TSFS spectra generated by the measurement: parallel (||), perpendicular (⊥), unpolarized (T) intensity spectra and anisotropy maps. TSFS_|| (parallel polarized) measurements were the best for protein quantification compared to standard unpolarized measurements and the Bradford assay. This was because TSFS_|| spectra had a better analyte signal to noise ratio (SNR), due to the anisotropy of protein emission. This meant that protein signals were better resolved from the background emission of small molecule fluorophores in the cell culture media. SNR of >5000 was achieved for concentrations of bovine serum albumin/yeastolate 1.2/10 g L^-1 with TSFS_|| . Optimization using genetic algorithm and interval partial least squares based variable selection enabled reduction of spectral resolution and number of excitation wavelengths required without degrading performance. This enables fast (<3.5 min) online/at-line measurements, and the method had an LOD of 0.18 g L^-1 and high accuracy with a predictive error of <9%.

Modelling Förster resonance energy transfer (FRET) using anisotropy resolved multi-dimensional emission spectroscopy (ARMES)

BACKGROUND

Förster Resonance Energy Transfer (FRET) is widely used to study the structure and dynamics of biomolecular systems and also causes the non-linear fluorescence response observed in multi-fluorophore proteins. Accurate FRET analysis, in terms of measuring changes in donor and acceptor spectra and energy transfer efficiency is therefore critical.

METHODS

We demonstrate a novel quantitative FRET analysis using anisotropy resolved multidimensional emission spectroscopy (ARMES) in a Human Serum Albumin (HSA) and 1,8-anilinonaphathalene sulfonate (ANS) model. ARMES combines 4D measurement of polarized excitation emission matrices (pEEM) with multivariate data analysis to spectrally resolve contributing fluorophores. Multivariate analysis (Parallel Factor, PARAFAC and restricted Tucker3) was used to resolve fluorophore contributions and for modelling the quenching of HSA emission and the HSA-ANS interactions.

RESULTS

pEEM spectra were modelled using Tucker3 which accommodates non-linearities introduced by FRET and a priori chemical knowledge was used to optimise the solution, thus resolving three components: HSA emission, ANS emission from indirect FRET excitation, and ANS emission from direct excitation. Perpendicular emission measurements were more sensitive to indirectly excited acceptor emission. PARAFAC modelling of HSA, donor emission, separated ANS FRET interacting (Tryptophan) and non-interacting (Tyrosine) components. This enabled a new way of calculating quenching constants using the multi-dimensional emission of individual donor fluorophores.

CONCLUSIONS

FRET efficiency could be calculated using the multi-dimensional, resolved emission of the interacting donor fluorophores only which yielded higher ET efficiencies compared to conventional methods.

GENERAL SIGNIFICANCE

Shows the potential of multidimensional fluorescence measurements and data analysis for more accurate FRET modelling in proteins.

Super Stable Fluorescein Isothiocyanate Isomer I Monolayer for Total Internal Reflection Fluorescence Microscopy

Total internal reflection fluorescence microscopy (TIRFM) is an important method in surface science and for the analysis of surface-bound macromolecules. Here, we developed and explored the use of a novel fluorescein isothiocyanate isomer I (FITC)-adsorbed monolayer for alignment and validation of TIRFM measurements and configurations. Aqueous solutions of FITC exist as several different protolytic forms (dianionic, anionic, neutral, and cationic) with each form having different emission characteristics. However, the emission behavior of FITC adsorbed on hydrophilic, hydrophobic, and unmodified glass surfaces at different pH was unknown. TIRFM imaging and spectroscopy were used to study FITC and FITC-labeled bovine serum albumin (BSA-FITC) monolayers generated on three different glass surfaces. Monolayer emission intensity, spectra, and the photobleaching profiles were all dependent on pH and the surface properties of the glass. Very strangely, however, at pH 5.0 on hydrophobic surfaces, the FITC monolayers produced were both bright and apparently unbleachable over ∼20 min of imaging (60 s total exposure). During monolayer formation at pH 5.0, we saw clear evidence for concentration-based quenching, indicating high surface coverage. When the monolayer had been rinsed with buffer to remove unbound FITC, we observed an increase in emission intensity during illumination indicative of some form of photoactivated species being present. Eventually, the fluorescence emission stabilized and remained constant for extended periods of time with no evidence of photobleaching. We hypothesize that during the adsorption process (a hydrophobic-hydrophobic interaction) there was conversion to the fluorescent quinoid form of FITC. In contrast, at pH 7.4 and 9.6 on hydrophobic surfaces, FITC monolayers had well-defined, fast photobleaching kinetics (decay to ∼50% intensity in 5-10 s). The equivalent BSA-FITC monolayers were slightly brighter, with similar photobleaching kinetics. While the precise mechanism for this unusual behavior is still unknown, all these low-cost monolayers were easily prepared, were reproducible, and can serve as convenient test samples for TIRFM alignment, calibration, and validation prior to undertaking measurements with more sensitive biogenic or biological specimens.

An excitation emission fluorescence lifetime spectrometer using a frequency doubled supercontinuum laser source

The accurate fluorescence analysis of complex, multi-fluorophore containing proteins requires the use of multi-dimensional measurement techniques. For the measurement of intrinsic fluorescence from tyrosine (Tyr) and tryptophan (Trp) one needs tuneable UV excitation and for steady-state measurements like Excitation Emission Matrix (EEM) simple pulsed Xe lamps are commonly used. Unfortunately, simultaneous multi-dimensional wavelength and time resolved measurement of intrinsic protein fluorescence in the 260 to 400 nm spectral range are challenging and typically required the use of very complex tuneable laser systems or multiple single excitation wavelength sources. Here we have assembled and validated a novel Excitation Emission Fluorescence Lifetime Spectrometer (EEFLS) using a pulsed, frequency doubled, Super-Continuum Laser (SCL) source coupled with a 16 channel multi-anode Time Correlated Single Photon Counting (TCSPC) measurement system. This EEFLS enabled the collection of near complete lifetime and intensity maps over the most important intrinsic protein fluorescence spectral range (λ _ex = 260-350/λ _em = 300-500 nm). The 4-dimensional (λ _ex/λ _em/I_(t)/τ) Excitation Emission Fluorescence Lifetime Matrix (EEFLM) data produced can be used to better characterize the complex intrinsic emission from proteins. The system was capable of measuring fluorescence emission data with high spectral (1-2 nm) resolution and had an Instrument Response Function (IRF) of ∼650 ps for accurate measurement of nanosecond lifetimes. UV power output was stable after a warm up period, with variations of <2% over 9 hours and reproducible (relative standard deviation RSD < 1.5%). This enabled the collection of accurate EEFLM data at low resolution (∼12 nm in excitation and emission) in 1-2 hours or high resolution (4 nm) in ∼17 hours. EEFLS performance in the UV was compared with a conventional commercial TCSPC system using pulsed LED excitation and validated using solutions of p-terphenyl and tryptophan.

Calibration, standardization, and quantitative analysis of multidimensional fluorescence (MDF) measurements on complex mixtures (IUPAC Technical Report)

This IUPAC Technical Report describes and compares the currently applied methods for the calibration and standardization of multi-dimensional fluorescence (MDF) spectroscopy data as well as recommendations on the correct use of chemometric methods for MDF data analysis. The paper starts with a brief description of the measurement principles for the most important MDF techniques and a short introduction to the most important applications. Recommendations are provided for instrument calibration, sample preparation and handling, and data collection, as well as the proper use of chemometric data analysis methods.

Extended wavelength anisotropy resolved multidimensional emission spectroscopy (ARMES) measurements: better filters, validation standards, and Rayleigh scatter removal methods

Anisotropy resolved multidimensional emission spectroscopy (ARMES) provides valuable insights into multi-fluorophore proteins (Groza et al 2015 Anal. Chim. Acta 886 133-42). Fluorescence anisotropy adds to the multidimensional fluorescence dataset information about the physical size of the fluorophores and/or the rigidity of the surrounding micro-environment. The first ARMES studies used standard thin film polarizers (TFP) that had negligible transmission between 250 and 290 nm, preventing accurate measurement of intrinsic protein fluorescence from tyrosine and tryptophan. Replacing TFP with pairs of broadband wire grid polarizers enabled standard fluorescence spectrometers to accurately measure anisotropies between 250 and 300 nm, which was validated with solutions of perylene in the UV and Erythrosin B and Phloxine B in the visible. In all cases, anisotropies were accurate to better than ±1% when compared to literature measurements made with Glan Thompson or TFP polarizers. Better dual wire grid polarizer UV transmittance and the use of excitation-emission matrix measurements for ARMES required complete Rayleigh scatter elimination. This was achieved by chemometric modelling rather than classical interpolation, which enabled the acquisition of pure anisotropy patterns over wider spectral ranges. In combination, these three improvements permit the accurate implementation of ARMES for studying intrinsic protein fluorescence.

Applications of Raman Spectroscopy in Biopharmaceutical Manufacturing: A Short Review

The production of active pharmaceutical ingredients (APIs) is currently undergoing its biggest transformation in a century. The changes are based on the rapid and dramatic introduction of protein- and macromolecule-based drugs (collectively known as biopharmaceuticals) and can be traced back to the huge investment in biomedical science (in particular in genomics and proteomics) that has been ongoing since the 1970s. Biopharmaceuticals (or biologics) are manufactured using biological-expression systems (such as mammalian, bacterial, insect cells, etc.) and have spawned a large (>€35 billion sales annually in Europe) and growing biopharmaceutical industry (BioPharma). The structural and chemical complexity of biologics, combined with the intricacy of cell-based manufacturing, imposes a huge analytical burden to correctly characterize and quantify both processes (upstream) and products (downstream). In small molecule manufacturing, advances in analytical and computational methods have been extensively exploited to generate process analytical technologies (PAT) that are now used for routine process control, leading to more efficient processes and safer medicines. In the analytical domain, biologic manufacturing is considerably behind and there is both a huge scope and need to produce relevant PAT tools with which to better control processes, and better characterize product macromolecules. Raman spectroscopy, a vibrational spectroscopy with a number of useful properties (nondestructive, non-contact, robustness) has significant potential advantages in BioPharma. Key among them are intrinsically high molecular specificity, the ability to measure in water, the requirement for minimal (or no) sample pre-treatment, the flexibility of sampling configurations, and suitability for automation. Here, we review and discuss a representative selection of the more important Raman applications in BioPharma (with particular emphasis on mammalian cell culture). The review shows that the properties of Raman have been successfully exploited to deliver unique and useful analytical solutions, particularly for online process monitoring. However, it also shows that its inherent susceptibility to fluorescence interference and the weakness of the Raman effect mean that it can never be a panacea. In particular, Raman-based methods are intrinsically limited by the chemical complexity and wide analyte-concentration-profiles of cell culture media/bioprocessing broths which limit their use for quantitative analysis. Nevertheless, with appropriate foreknowledge of these limitations and good experimental design, robust analytical methods can be produced. In addition, new technological developments such as time-resolved detectors, advanced lasers, and plasmonics offer potential of new Raman-based methods to resolve existing limitations and/or provide new analytical insights.

Kernel principal component analysis residual diagnosis (KPCARD): An automated method for cosmic ray artifact removal in Raman spectra

A new, fully automated, rapid method, referred to as kernel principal component analysis residual diagnosis (KPCARD), is proposed for removing cosmic ray artifacts (CRAs) in Raman spectra, and in particular for large Raman imaging datasets. KPCARD identifies CRAs via a statistical analysis of the residuals obtained at each wavenumber in the spectra. The method utilizes the stochastic nature of CRAs; therefore, the most significant components in principal component analysis (PCA) of large numbers of Raman spectra should not contain any CRAs. The process worked by first implementing kernel PCA (kPCA) on all the Raman mapping data and second accurately estimating the inter- and intra-spectrum noise to generate two threshold values. CRA identification was then achieved by using the threshold values to evaluate the residuals for each spectrum and assess if a CRA was present. CRA correction was achieved by spectral replacement where, the nearest neighbor (NN) spectrum, most spectroscopically similar to the CRA contaminated spectrum and principal components (PCs) obtained by kPCA were both used to generate a robust, best curve fit to the CRA contaminated spectrum. This best fit spectrum then replaced the CRA contaminated spectrum in the dataset. KPCARD efficacy was demonstrated by using simulated data and real Raman spectra collected from solid-state materials. The results showed that KPCARD was fast (<1 min per 8400 spectra), accurate, precise, and suitable for the automated correction of very large (>1 million) Raman datasets.

Anisotropy resolved multidimensional emission spectroscopy (ARMES): A new tool for protein analysis

Structural analysis of proteins using the emission of intrinsic fluorophores is complicated by spectral overlap. Anisotropy resolved multidimensional emission spectroscopy (ARMES) overcame the overlap problem by the use of anisotropy, with chemometric analysis, to better resolve emission from different fluorophores. Total synchronous fluorescence scan (TSFS) provided information about all the fluorophores that contributed to emission while anisotropy provided information about the environment of each fluorophore. Here the utility of ARMES was demonstrated via study of the chemical and thermal denaturation of human serum albumin (HSA). Multivariate curve resolution (MCR) analysis of the constituent polarized emission ARMES data resolved contributions from four emitters: fluorescence from tryptophan (Trp), solvent exposed tyrosine (Tyr), Tyr in a hydrophobic environment, and room temperature phosphorescence (RTP) from Trp. The MCR scores, anisotropy, and literature validated these assignments and showed all the expected transitions during HSA unfolding. This new methodology for comprehensive intrinsic fluorescence analysis of proteins is applicable to any protein containing multiple fluorophores.

A fluorescence anisotropy method for measuring protein concentration in complex cell culture media

The rapid, quantitative analysis of the complex cell culture media used in biopharmaceutical manufacturing is of critical importance. Requirements for cell culture media composition profiling, or changes in specific analyte concentrations (e.g. amino acids in the media or product protein in the bioprocess broth) often necessitate the use of complicated analytical methods and extensive sample handling. Rapid spectroscopic methods like multi-dimensional fluorescence (MDF) spectroscopy have been successfully applied for the routine determination of compositional changes in cell culture media and bioprocess broths. Quantifying macromolecules in cell culture media is a specific challenge as there is a need to implement measurements rapidly on the prepared media. However, the use of standard fluorescence spectroscopy is complicated by the emission overlap from many media components. Here, we demonstrate how combining anisotropy measurements with standard total synchronous fluorescence spectroscopy (TSFS) provides a rapid, accurate quantitation method for cell culture media. Anisotropy provides emission resolution between large and small fluorophores while TSFS provides a robust measurement space. Model cell culture media was prepared using yeastolate (2.5 mg mL(-1)) spiked with bovine serum albumin (0 to 5 mg mL(-1)). Using this method, protein emission is clearly discriminated from background yeastolate emission, allowing for accurate bovine serum albumin (BSA) quantification over a 0.1 to 4.0 mg mL(-1) range with a limit of detection (LOD) of 13.8 μg mL(-1).

Comprehensive, quantitative bioprocess productivity monitoring using fluorescence EEM spectroscopy and chemometrics

Using fluorescence excitation-emission matrix spectroscopy and chemometric methods we demonstrate an effective and rapid method for quantitative monitoring of a mammalian cell culture based manufacturing process.

A family of [Ni8] cages templated by μ6-peroxide from dioxygen activation

[Ni₈] cages templated by η³:η³:μ₆-O₂²⁻ from O₂ activation: the ligand found oxidized within the cages.

Quantitative polymorph contaminant analysis in tablets using Raman and near infra-red spectroscopies

The detection and quantification of alternate polymorphs of active pharmaceutical ingredients (APIs), particularly at low concentrations is a key issue for the manufacture and analysis of solid-state formulations. Each polymorph can possess unique physical and chemical properties which in turn can directly affect factors such as solubility and bioavailability. Near infra-red (NIR) and Raman spectroscopies can be used for the rapid characterisation and quantification of polymorphs in solid samples. In this study we have generated a model tablet system with two excipients and a 10% API concentration, where the API is a mixture of the FII and FIII polymorphs of piracetam. Using transmission Raman spectroscopy (TRS) and NIR spectroscopy it was possible to detect FII polymorph contamination in these model tablets with limits of detection (LODs) of 0.6 and 0.7%, respectively, with respect to the total tablet weight (or ∼6-7% of the API content). The TRS method is the superior method because of the speed of analysis (∼6s per sample), better sampling statistics, and because the sharper, more resolved bands in the Raman spectra allowed for easier interpretation of the spectral data. In addition the TRS used here provides facile access to the low frequency wavenumber region for analysis of solid-state lattice modes.

Cell cycle-dependent mobility of Cdc45 determined in vivo by fluorescence correlation spectroscopy

Eukaryotic DNA replication is a dynamic process requiring the co-operation of specific replication proteins. We measured the mobility of eGFP-Cdc45 by Fluorescence Correlation Spectroscopy (FCS) in vivo in asynchronous cells and in cells synchronized at the G1/S transition and during S phase. Our data show that eGFP-Cdc45 mobility is faster in G1/S transition compared to S phase suggesting that Cdc45 is part of larger protein complex formed in S phase. Furthermore, the size of complexes containing Cdc45 was estimated in asynchronous, G1/S and S phase-synchronized cells using gel filtration chromatography; these findings complemented the in vivo FCS data. Analysis of the mobility of eGFP-Cdc45 and the size of complexes containing Cdc45 and eGFP-Cdc45 after UVC-mediated DNA damage revealed no significant changes in diffusion rates and complex sizes using FCS and gel filtration chromatography analyses. This suggests that after UV-damage, Cdc45 is still present in a large multi-protein complex and that its mobility within living cells is consistently similar following UVC-mediated DNA damage.

Fluorescence excitation-emission matrix (EEM) spectroscopy for rapid identification and quality evaluation of cell culture media components

The application of fluorescence excitation-emission matrix (EEM) spectroscopy to the quantitative analysis of complex, aqueous solutions of cell culture media components was investigated. These components, yeastolate, phytone, recombinant human insulin, eRDF basal medium, and four different chemically defined (CD) media, are used for the formulation of basal and feed media employed in the production of recombinant proteins using a Chinese Hamster Ovary (CHO) cell based process. The comprehensive analysis (either identification or quality assessment) of these materials using chromatographic methods is time consuming and expensive and is not suitable for high-throughput quality control. The use of EEM in conjunction with multiway chemometric methods provided a rapid, nondestructive analytical method suitable for the screening of large numbers of samples. Here we used multiway robust principal component analysis (MROBPCA) in conjunction with n-way partial least squares discriminant analysis (NPLS-DA) to develop a robust routine for both the identification and quality evaluation of these important cell culture materials. These methods are applicable to a wide range of complex mixtures because they do not rely on any predetermined compositional or property information, thus making them potentially very useful for sample handling, tracking, and quality assessment in biopharmaceutical industries.

Qualitative analysis using Raman spectroscopy and chemometrics: a comprehensive model system for narcotics analysis

The rapid, on-site identification of illicit narcotics, such as cocaine, is hindered by the diverse nature of the samples, which can contain a large variety of materials in a wide concentration range. This sample variance has a very strong influence on the analytical methodologies that can be utilized and in general prevents the widespread use of quantitative analysis of illicit narcotics on a routine basis. Raman spectroscopy, coupled with chemometric methods, can be used for in situ qualitative and quantitative analysis of illicit narcotics; however, careful consideration must be given to dealing with the extensive variety of sample types. To assess the efficacy of combining Raman spectroscopy and chemometrics for the identification of a target analyte under real-world conditions, a large-scale model sample system (633 samples) using a target (acetaminophen) mixed with a wide variety of excipients was created. Materials that exhibit problematic factors such as fluorescence, variable Raman scattering intensities, and extensive peak overlap were included to challenge the efficacy of chemometric data preprocessing and classification methods. In contrast to spectral matching analyte identification approaches, we have taken a chemometric classification model-based approach to account for the wide variances in spectral data. The first derivative of the Raman spectra from the fingerprint region (750-1900 cm(-1)) yielded the best classifications. Using a robust segmented cross-validation method, correct classification rates of better than ∼90% could be attained with regression-based classification, compared to ∼35% for SIMCA. This study demonstrates that even with very high degrees of sample variance, as evidenced by dramatic changes in Raman spectra, it is possible to obtain reasonably reliable identification using a combination of Raman spectroscopy and chemometrics. The model sample set can now be used to validate more advanced chemometric or machine learning algorithms being developed for the identification of analytes such as illicit narcotics.

Measuring the micro-polarity and hydrogen-bond donor/acceptor ability of thermoresponsive N-isopropylacrylamide/N-tert-butylacrylamide copolymer films using solvatochromic indicators

Thin polymer films are important in many areas of biomaterials research, biomedical devices, and biological sensors. The accurate in situ measurement of multiple physicochemical properties of thin polymer films is critical in understanding biocompatibility, polymer function, and performance. In this work we demonstrate a facile spectroscopic methodology for accurately measuring the micro-polarity and hydrogen-bond donor/acceptor ability for a series of relatively hydrophilic thermoresponsive copolymers. The micro-polarity of the N-isopropylacrylamide (NIPAM) and N-tert-butylacrylamide (NtBA) co-polymers was evaluated by means of the E(T)(30), alpha, beta, and pi empirical solvatochromic polarity parameters. The data shows that increasing the NtBA fraction in the dry copolymer film reduces polarity and hydrogen-bonding ability. Within the Kamlet-Taft polarity framework, the NIPAM/NtBA copolymer films are strong hydrogen-bond acceptors, strongly dipolar/polarizable, and rather moderate hydrogen-bond donors. This characterization provides a more comprehensive physicochemical description of polymers, which aids the interpretation of film performance. Comparison of the measured E(T)(30) values with literature data for other water-soluble polymers show that dry NIPAM/NtBA copolymers are slightly more polar than poly(ethylene oxide), less polar than polyvinylalcohol, and approximately the same polarity as poly(N-vinyl-2-pyrrolidone). These findings indicate that this spectroscopic method is a facile, rapid, and nondestructive methodology for measuring polymer properties in situ, suitable for most biomaterials research laboratories.

Mobility and distribution of replication protein A in living cells using fluorescence correlation spectroscopy

Replication protein A (RPA), the eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for all pathways of DNA metabolism. To study the function of RPA in living cells the second largest RPA subunit and an N-terminal deletion mutant thereof were fused to green fluorescent protein (GFP; GFP-RPA2 and GFP-RPA2deltaN, respectively) in a controlled, molecular biological way. These proteins were expressed in HeLa cells under the control of the inducible tetracycline expression system. GFP-RPA2 and GFP-RPA2deltaN are predominately nuclear proteins as determined by confocal laser scanning microscopy. Low basal expression of GFP-RPA2deltaN allowed the measurement of kinetic parameters of RPA. Using fluorescence correlation spectroscopy (FCS) two populations--a fast and a slow moving species--were detected in the nucleus and the cytosol of human cells. The translational diffusion rates of these two RPA populations were approximately 15 microm2/s and 1.8 microm2/s. This new finding reveals the existence of different multiprotein and ssDNA-protein complexes of RPA in both cellular compartments and opens the possibility for their analyses.

Fluorescence lifetime imaging study of a thin protein layer on solid surfaces

Understanding the fundamental interactions between proteins and solid surfaces is essential in the area of implantable medical devices. Fluorescence methods offer the sensitivity required to study the formation of the initial thin protein layers that mediate biocompatibility of materials. Thin protein layers (bovine serum albumin labelled with 1-anilino-8-naphthalenesulfonate, BSA-ANS) deposited on several surfaces (glass, silicon, stainless steel, polystyrene, and silver island film) were studied using confocal frequency domain Fluorescence Lifetime Imaging Microscopy (FLIM) and single-point multifrequency lifetime analysis techniques. FLIM provides spatial information about both fluorophores located on the surface and physicochemical parameters of the surface microenvironment. The average fluorescence lifetimes (tau(av)) of the adsorbed BSA-ANS generated by the contact between a protein solution and the material surface were measured by the multifrequency modulation and phase shift. Results indicate that tau(av) values of the albumin complexes on the surfaces (approximately 12 ns) are, in general, shorter than tau(av) found in the bulk solution (approximately 14 ns). For some surfaces, like polystyrene and silver island film the differences in tau(av) of the adsorbed BSA-ANS were found to be much greater. The differences in fluorescence lifetimes may indicate structural changes in the BSA protein induced by contact with the surface.

Comparison of derivative preprocessing and automated polynomial baseline correction method for classification and quantification of narcotics in solid mixtures

This work offers a real-world comparison of derivative preprocessing and a new polynomial method described by Lieber and Mahadevan-Jansen (LMJ) for baseline correction of Raman spectra with widely varying backgrounds. This comparison is based on their outcomes in factor analysis, analyte discrimination, and quantification. Both correction methods are applied to a Raman spectra data set taken from 85 solid samples of illegal narcotics diluted with various materials. It is found that neither approach outperforms the other, as they give similar principal component analysis (PCA) models and quantification errors: cocaine and heroin show cross-validation errors of approximately 8%, while MDMA is quantified to a cross-validation error of approximately 3-4%. The LMJ method does offer several other advantages, the most significant being the retention of original peak shapes after the correction, which simplifies the interpretation of the preprocessed spectra. The LMJ method is therefore recommended for use as a baseline correction method in future research with Raman spectroscopy.

Surface enhanced Raman scattering for narcotic detection and applications to chemical biology

Raman spectroscopy is rapidly finding favour for applications in the life science because of the ease with which it can be used to extract significant data from tissue and cells. However, the Raman effect is an inherently weak effect, which hinders the analysis of low concentration analytes. Raman sensitivity can be improved via the surface enhanced Raman scattering (SERS) effect. In SERS, Raman spectra are dramatically amplified when a molecule is adsorbed onto nano-roughened noble metal surfaces such as silver and gold. The degree of enhancement enables single-molecule detection, which offers the potential for the unambiguous identification of analytes at concentrations that are useful in both a forensic and a chemical biology context. Here we discuss some of the practical applications of SERS to both low-level narcotic detection, and how this can be applied to chemical biology.

Time-resolved fluorescence studies on bovine serum albumin denaturation process

The denaturation of Bovine Serum Albumin (BSA) by a chaotropic agent, guanidinium hydrochloride (GuH+Cl-) was studied by fluorescence lifetime analysis. The BSA was labelled with 1-anilino-8-naphthalene sulfonate (ANS) at two different molar ratios (1:1) and (1:10). The non-exponential fluorescence kinetics of the BSA-ANS complex at different stages of denaturation is analysed using three different models: a discrete tri-exponential sum, stretched exponential, and Gaussian lifetime distribution. In all cases, the fluorescence decay times decreased with protein denaturation. The results from the models show that there are at least two different binding sites located in the BSA protein with different water accessibility.

Determination of the modulation transfer function for a time-gated fluorescence imaging system

The use of fluorescence for cancer detection is currently under investigation. Presently, steady-state fluorescence detection methods are in use, but have limitations due to poor contrast between the fluorescence of the tumor and background autofluorescence. Improved contrast can be obtained with time-resolved techniques because of the differing lifetimes between autofluorescence and exogenous photosensitizers that selectively accumulate within tumor tissue. An imaging system is constructed using a fast-gated (200-ps) charge-coupled device (CCD) camera and a pulsed 635-nm laser diode. To characterize the ability of the system to transfer object contrast to an image, the modulation transfer function (MTF) of the system is acquired by employing an extended knife-edge technique. A knife-edge target is assembled by drilling a rectangular well into a block of polymethyl methacrylate (PMMA). The imaging system records images of the photosensitizer, chloroaluminum phthalocyanine tetrasulfonate (AlPcTS), within the well. AlPcTS was chosen to test the system because of its strong absorption of 635-nm, high fluorescence yield, and relatively long fluorescence lifetime (approximately 7.5 ns). The results show that the system is capable of resolving 10(-4) M AlPcTS fluorescence as small as 1 mm. The findings of this study contribute to the development of a time-gated imaging system using fluorescence lifetimes.

Time-resolved fluorescence microspectroscopy for characterizing crude oils in bulk and hydrocarbon-bearing fluid inclusions

Time-resolved fluorescence data was collected from a series of 23 bulk crude petroleum oils and six microscopic hydrocarbon-bearing fluid inclusions (HCFI). The data was collected using a diode laser fluorescence lifetime microscope (DLFLM) over the 460-700 nm spectral range using a 405 nm excitation source. The correlation between intensity averaged lifetimes (tau) and chemical and physical parameters was examined with a view to developing a quantitative model for predicting the gross chemical composition of hydrocarbon liquids trapped in HCFI. It was found that tau is nonlinearly correlated with the measured polar and corrected alkane concentrations and that oils can be classified on this basis. However, these correlations all show a large degree of scatter, preventing accurate quantitative prediction of gross chemical composition of the oils. Other parameters such as API gravity and asphaltene, aromatic, and sulfur concentrations do not correlate well with tau measurements. Individual HCFI were analyzed using the DLFLM, and time-resolved fluorescence measurements were compared with tau data from the bulk oils. This enabled the fluid within the inclusions to be classified as either low alkane/high polar or high alkane/low polar. Within the high alkane/low polar group, it was possible to clearly discriminate HCFI from different locales and to see differences in the trapped hydrocarbon fluids from a single geological source. This methodology offers an alternative method for classifying the hydrocarbon content of HCFI and observing small variations in the trapped fluid composition that is less sensitive to fluctuations in the measurement method than fluorescence intensity based methods.

Time-resolved fluorescence spectroscopic study of crude petroleum oils: influence of chemical composition

The fluorescence of crude petroleum oils is sensitive to changes in chemical composition and many different fluorescence methods have been used to characterize crude oils. The use of fluorescence lifetimes to quantitatively characterize oil composition has practical advantages over steady-state measurements, but there have been comparatively few studies in which the lifetime behavior is correlated with gross chemical compositional data. In this study, the fluorescence lifetimes for a series of 23 crude petroleum oils with American Petroleum Institute (API) gravities of between 10 and 50 were measured at several emission wavelengths (450-785 nm) using a 380 nm light emitting diode (LED) excitation source. It was found that the intensity average fluorescence lifetime (tau) at any emission wave-length does not correlate well with either API gravity or aromatic concentration. However, it was found that tau is strongly negatively correlated with both the polar and sulfur concentrations and positively correlated with the corrected alkane concentration. This indicates that the fluorescence behavior of crude petroleum oils is governed primarily by the concentration of quenching species. All the strong lifetime-concentration correlations are nonlinear and show a high degree of scatter, especially for medium to light oils with API gravities of between 25 and 40. The degree of scatter is greatest for oils where the concentrations (wt %) of the polar fraction is approximately 10 +/- 4%, the asphaltene component is approximately 1 +/- 0.5%, and sulfur is 0.5 +/- 0.4%. This large degree of scatter precludes the use of average fluorescence lifetime data obtained with 380 nm excitation for the accurate prediction of the common chemical compositional parameters of crude petroleum oils.

The use of chloroaluminium phthalocyanine tetrasulfonate (AlPcTS) for time-delayed fluorescence imaging

Phthalocyanine derivatives are currently under investigation for use in photodynamic therapy, which is a promising cancer treatment. These materials, which display preferential uptake in cancerous cells, also exhibit high fluorescence yields and can be used for tumour detection. Problems with steady-state fluorescence techniques such as excitation scatter and background autofluorescence can be eliminated by using time-resolved imaging techniques without the need for filters. A tissue phantom was assembled to test a constructed time-gated imaging system by drilling 36 wells of varying diameter and depth (10 mm to 1 mm) into a block of polymethyl methacrylate (PMMA). The system was used to record images of chloroaluminium phthalocyanine tetrasulfonate (AlPcTS) at differing concentrations in neat aqueous solvent and cell suspensions within the wells. A mixture of Intralipid (to mimic tissue scatter) and Evan's blue (to mimic tissue absorption) of depths ranging from 1 mm to 10 mm was placed on top of the PMMA block. The ensuing images were analysed using signal-to-noise ratios and contrast-detail curves. The results indicate that the time-gated imaging system can prevent background excitation scatter from distorting the fluorescence signal from a longer-lived photosensitizer without the need for filters.

Assessing the Maturity of Crude Petroleum Oils Using Total Synchronous Fluorescence Scan Spectra

There have been many applications of fluorescence methods for the analysis of crude petroleum oils down through the years. However, none of these studies has yielded a robust qualitative or quantitative method for quantifying the chemical composition, or assessing the maturity of crude oils. Simple fluorescence parameters such as lifetime, intensity, and intensity ratios do not correlate well with chemical composition particularly for medium weight crude oils [A. G. Ryder, T. J. Glynn, and M. Feely (2003). Proc. SPIE-Int. Soc. Opt. Eng. 4876, 1188-1195.]. A better approach may be to use the Total Synchronous Fluorescence Scan (TSFS) method to fully interrogate the complex chemical composition of the oils [D. Patra and A. K. Mishra (2002). Anal. Bioanal. Chem. 373, 304-309.]. We present TSFS spectra from 18 crude petroleum oils of varying composition, sourced from around the world. The TSFS plots of these oils are very complex, with the contours being spread over the full 250-700 nm wavelength range (lambda(ex)) and 40-200 nm wavelength interval (delta lambda) sampled. The 3-D contour maps tend to two contour concentrations one at lambda(em) < 300 nm, delta lambda = 120-200 nm, and a second near lambda(ex) approximately 380-400 nm, delta lambda = 40-60 nm. The first feature represents fluorescence emission originating mainly from energy transfer processes with the second, longer wavelength feature originating from fluorescence emission generated by a higher proportion of direct excitation as opposed to emission resulting from energy transfer. The topography of the 3D contour plots is therefore influenced by the balance between energy transfer and direct fluorescence emission, which is governed by the chemical composition of the crude oils. We discuss how the gross chemical composition affects TSFS spectra and how TSFS can be used to assess oil maturity with a view to developing quantitative methods.

Evaluation of acridine in Nafion as a fluorescence-lifetime-based pH sensor

We report a novel fluorescence-lifetime-based pH sensing method that utilizes acridine incorporated into Nafion (AcNaf) as the fluorescent indicator. The AcNaf sensor is excited using a 380 nm light emitting diode (LED) and the fluorescence lifetimes are measured at 450 and 500 nm. The fluorescence behavior of acridine as a function of pH in aqueous phosphate buffers and incorporated into the Nafion membrane has been investigated. The results show that incorporating acridine into Nafion changes the apparent ground-state pKa from -5.45 to -9, while the apparent excited-state pKa* is only slightly changed (approximately 9.4 in 0.1 M phosphate buffer). The AcNaf film shows a good pH response with a change in average lifetime of approximately 19 ns (at an emission wavelength of 450 nm) over the pH 8 to 10 range. We also show that excited-state protonation does not occur in the AcNaf sensor film and that chloride quenching cannot occur because of the permselective nature of Nafion. We also discuss how the unique structure of Nafion affects the fluorescence behavior of acridine at various pH values and examine the impact of buffer concentration on apparent pKa and pH sensing ability.