Ultrasound-enhanced attenuated total reflection mid-infrared spectroscopy in-line probe: acquisition of cell spectra in a bioreactor

Exploration of macromolecular phenotype of human skeletal muscle in diabetes using infrared spectroscopy

Introduction

The global burden of diabetes mellitus is escalating, and more efficient investigative strategies are needed for a deeper understanding of underlying pathophysiological mechanisms. The crucial role of skeletal muscle in carbohydrate and lipid metabolism makes it one of the most susceptible tissues to diabetes-related metabolic disorders. In tissue studies, conventional histochemical methods have several technical limitations and have been shown to inadequately characterise the biomolecular phenotype of skeletal muscle to provide a holistic view of the pathologically altered proportions of macromolecular constituents.

Materials and methods

In this pilot study, we examined the composition of five different human skeletal muscles from male donors diagnosed with type 2 diabetes and non-diabetic controls. We analysed the lipid, glycogen, and collagen content in the muscles in a traditional manner with histochemical assays using different staining techniques. This served as a reference for comparison with the unconventional analysis of tissue composition using Fourier-transform infrared spectroscopy as an alternative methodological approach.

Results

A thorough chemometric post-processing of the infrared spectra using a multi-stage spectral decomposition allowed the simultaneous identification of various compositional details from a vibrational spectrum measured in a single experiment. We obtained multifaceted information about the proportions of the different macromolecular constituents of skeletal muscle, which even allowed us to distinguish protein constituents with different structural properties. The most important methodological steps for a comprehensive insight into muscle composition have thus been set and parameters identified that can be used for the comparison between healthy and diabetic muscles.

Conclusion

We have established a methodological framework based on vibrational spectroscopy for the detailed macromolecular analysis of human skeletal muscle that can effectively complement or may even serve as an alternative to histochemical assays. As this is a pilot study with relatively small sample sets, we remain cautious at this stage in drawing definitive conclusions about diabetes-related changes in skeletal muscle composition. However, the main focus and contribution of our work has been to provide an alternative, simple and efficient approach for this purpose. We are confident that we have achieved this goal and have brought our methodology to a level from which it can be successfully transferred to a large-scale study that allows the effects of diabetes on skeletal muscle composition and the interrelationships between the macromolecular tissue alterations due to diabetes to be investigated.

Current and future technologies for monitoring cultured meat: A review

The high population growth rate, massive animal food consumption, fast economic progress, and limited food resources could lead to a food crisis in the future. There is a huge requirement for dietary proteins including cultured meat is being progressed to fulfill the need for meat-derived proteins in the diet. However, production of cultured meat requires monitoring numerous bioprocess parameters. This review presents a comprehensive overview of various widely adopted techniques (optical, spectroscopic, electrochemical, capacitive, FETs, resistive, microscopy, and ultrasound) for monitoring physical, chemical, and biological parameters that can improve the bioprocess control in cultured meat. The methods, operating principle, merits/demerits, and the main open challenges are reviewed with the aim to support the readers in advancing knowledge on novel sensing systems for cultured meat applications.

Rapid and accurate screening of cystic echinococcosis in sheep based on serum Fourier-transform infrared spectroscopy combined with machine learning algorithms

Cystic echinococcosis (CE) in sheep is a serious zoonotic parasitic disease caused by Echinococcus granulosus sensu stricto (s.s.). Presently, the screening technology for CE in sheep is time-consuming and inaccurate, and novel screening technology is urgently needed. In this work, we combined machine-learning algorithms with Fourier transform infrared (FT-IR) spectroscopy of serum to establish a quick and accurate screening approach for CE in sheep. Serum samples from 77 E. granulosus s.s.-infected sheep to 121 healthy control sheep were measured by FT-IR spectrometer. To optimize the classification accuracy of the serum FI-TR method for the E. granulosus s.s.-infected sheep and healthy control sheep, principal component analysis (PCA), linear discriminant analysis, and support vector machine (SVM) algorithms were used to analyze the data. Among all the bands, 1500-1700 cm^-1 band has the best classification effect; its diagnostic sensitivity, specificity, and accuracy of PCA-SVM were 100%, 95.74%, and 96.66%, respectively. The study showed that serum FT-IR spectroscopy combined with machine learning algorithms has great potential for rapid and accurate screening methods for the CE in sheep.

Application of FTIR Spectroscopy to Detect Changes in Skeletal Muscle Composition Due to Obesity with Insulin Resistance and STZ-Induced Diabetes

Age, obesity, and diabetes mellitus are pathophysiologically interconnected factors that significantly contribute to the global burden of non-communicable diseases. These metabolic conditions are associated with impaired insulin function, which disrupts the metabolism of carbohydrates, lipids, and proteins and can lead to structural and functional changes in skeletal muscle. Therefore, the alterations in the macromolecular composition of skeletal muscle may provide an indication of the underlying mechanisms of insulin-related disorders. The aim of this study was to investigate the potential of Fourier transform infrared (FTIR) spectroscopy to reveal the changes in macromolecular composition in weight-bearing and non-weight-bearing muscles of old, obese, insulin-resistant, and young streptozotocin (STZ)-induced diabetic mice. The efficiency of FTIR spectroscopy was evaluated by comparison with the results of gold-standard histochemical techniques. The differences in biomolecular phenotypes and the alterations in muscle composition in relation to their functional properties observed from FTIR spectra suggest that FTIR spectroscopy can detect most of the changes observed in muscle tissue by histochemical analyses and more. Therefore, it could be used as an effective alternative because it allows for the complete characterization of macromolecular composition in a single, relatively simple experiment, avoiding some obvious drawbacks of histochemical methods.

Diamond-Coated Silicon ATR Elements for Process Analytics

Infrared attenuated total reflection (ATR) spectroscopy is a common laboratory technique for the analysis of highly absorbing liquids or solid samples. However, ATR spectroscopy is rarely found in industrial processes, where inline measurement, continuous operation, and minimal maintenance are important issues. Most materials for mid-infrared (MIR) spectroscopy and specifically for ATR elements do not have either high enough infrared transmission or sufficient mechanical and chemical stability to be exposed to process fluids, abrasive components, and aggressive cleaning agents. Sapphire is the usual choice for infrared wavelengths below 5 µm, and beyond that, only diamond is an established material. The use of diamond coatings on other ATR materials such as silicon will increase the stability of the sensor and will enable the use of larger ATR elements with increased sensitivity at lower cost for wavelengths above 5 µm. Theoretical and experimental investigations of the dependence of ATR absorbances on the incidence angle and thickness of nanocrystalline diamond (NCD) coatings on silicon were performed. By optimizing the coating thickness, a substantial amplification of the ATR absorbance can be achieved compared to an uncoated silicon element. Using a compact FTIR instrument, ATR spectra of water, acetonitrile, and propylene carbonate were measured with planar ATR elements made of coated and uncoated silicon. Compared to sapphire, the long wavelength extreme of the spectral range is extended to approximately 8 μm. With effectively nine ATR reflections, the sensitivity is expected to exceed the performance of typical diamond tip probes.

In Situ Quantification of Polyhydroxybutyrate in Photobioreactor Cultivations of Synechocystis sp. Using an Ultrasound-Enhanced ATR-FTIR Spectroscopy Probe

Polyhydroxybutyrate (PHB) is a very promising alternative to most petroleum-based plastics with the huge advantage of biodegradability. Biotechnological production processes utilizing cyanobacteria as sustainable source of PHB require fast in situ process analytical technology (PAT) tools for sophisticated process monitoring. Spectroscopic probes supported by ultrasound particle traps provide a powerful technology for in-line, nondestructive, and real-time process analytics in photobioreactors. This work shows the great potential of using ultrasound particle manipulation to improve spectroscopic attenuated total reflection Fourier-transformed mid-infrared (ATR-FTIR) spectra as a monitoring tool for PHB production processes in photobioreactors.

A thermoelectrically stabilized aluminium acoustic trap combined with attenuated total reflection infrared spectroscopy for detection of Escherichia coli in water

Acoustic trapping is a non-contact particle manipulation method that holds great potential for performing automated assays. We demonstrate an aluminium acoustic trap in combination with attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) for detection of E. coli in water. The thermal conductivity of aluminium was exploited to thermo-electrically heat and hold the acoustic trap at the desired assay temperature of 37 °C. Systematic characterisation and optimisation of the acoustic trap allowed high flow rates while maintaining high acoustic trapping performance. The ATR element serves not only as a reflector for ultrasound standing wave generation but also as a sensing interface. The enzyme conversion induced by alkaline phosphatase-labelled bacteria was directly monitored in the acoustic trap using ATR-FTIR spectroscopy. Sequential injection analysis allowed automated liquid handling, including non-contact bacteria retention, washing and enzyme-substrate exchange within the acoustic trap. The presented method was able to detect E. coli concentrations as low as 1.95 × 106 bacteria per mL in 197 min. The demonstrated ultrasound assisted assay paves the way to fully automated bacteria detection devices based on acoustic trapping combined with ATR-FTIR spectroscopy.

Monitoring E. coli Cell Integrity by ATR-FTIR Spectroscopy and Chemometrics: Opportunities and Caveats

During recombinant protein production with E. coli, the integrity of the inner and outer membrane changes, which leads to product leakage (loss of outer membrane integrity) or lysis (loss of inner membrane integrity). Motivated by current Quality by Design guidelines, there is a need for monitoring tools to determine leakiness and lysis in real-time. In this work, we assessed a novel approach to monitoring E. coli cell integrity by attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Various preprocessing strategies were tested in combination with regression (partial least squares, random forest) or classification models (partial least squares discriminant analysis, linear discriminant analysis, random forest, artificial neural network). Models were validated using standard procedures, and well-performing methods were additionally scrutinized by removing putatively important features and assessing the decrease in performance. Whereas the prediction of target compound concentration via regression was unsuccessful, possibly due to a lack of samples and low sensitivity, random forest classifiers achieved prediction accuracies of over 90% within the datasets tested in this study. However, strong correlations with untargeted spectral regions were revealed by feature selection, thereby demonstrating the need to rigorously validate chemometric models for bioprocesses, including the evaluation of feature importance.

Monitoring and control of E. coli cell integrity

Soluble expression of recombinant proteins in E. coli is often done by translocation of the product across the inner membrane (IM) into the periplasm, where it is retained by the outer membrane (OM). While the integrity of the IM is strongly coupled to viability and impurity release, a decrease in OM integrity (corresponding to increased "leakiness") leads to accumulation of product in the extracellular space, strongly impacting the downstream process. Whether leakiness is desired or not, differential monitoring and control of IM and OM integrity are necessary for an efficient E. coli bioprocess in compliance with the guidelines of Quality by Design and Process Analytical Technology. In this review, we give an overview of relevant monitoring tools, summarize the research on factors affecting E. coli membrane integrity and provide a brief discussion on how the available monitoring technology can be implemented in real-time control of E. coli cultivations.

Production of Active Recombinant Hyaluronidase Inclusion Bodies from Apis mellifera in E. coli Bl21(DE3) and characterization by FT-IR Spectroscopy

The bacterium E. coli is one of the most important hosts for recombinant protein production. The benefits are high growth rates, inexpensive media, and high protein titers. However, complex proteins with high molecular weight and many disulfide bonds are expressed as inclusion bodies (IBs). In the last decade, the overall perception of these IBs being not functional proteins changed, as enzyme activity was found within IBs. Several applications for direct use of IBs are already reported in literature. While fluorescent proteins or protein tags are used for determination of IB activity to date, direct measurements of IB protein activity are scacre. The expression of recombinant hyaluronidase from Apis mellifera in E. coli BL21(DE3) was analyzed using a face centered design of experiment approach. Hyaluronidase is a hard to express protein and imposes a high metabolic burden to the host. Conditions giving a high specific IB titer were found at 25 °C at low specific substrate uptake rates and induction times of 2 to 4 h. The protein activity of hyaluronidase IBs was verified using (Fourier transform) FT-IR spectroscopy. Degradation of the substrate hyaluronan occurred at increased rates with higher IB concentrations. Active recombinant hyaluronidase IBs can be immediately used for direct degradation of hyaluronan without further down streaming steps. FT-IR spectroscopy was introduced as a method for tracking IB activity and showed differences in degradation behavior of hyaluronan dependent on the applied active IB concentration.

Controllable Interfacial Polymerization for Nanofiltration Membrane Performance Improvement by the Polyphenol Interlayer

It is a huge challenge to have a controllable interfacial polymerization in the fabrication process of nanofiltration (NF) membranes. In this work, a polyphenol interlayer consisting of polyethyleneimine (PEI)/tannic acid (TA) was simply assembled on the polysulfone (PSf) substrate to fine-tune the interfacial polymerization process, without additional changes to the typical NF membrane fabrication procedures. In addition, three decisive factors in the interfacial polymerization process were examined, including the diffusion kinetics of fluorescence-labeled piperazine (FITC-PIP), the spreading behavior of the hexane solution containing acyl chloride, and the polyamide layer formation on the porous substrate by in situ Fourier transform infrared (FT-IR) spectroscopy. The experimental results demonstrate that the diffusion kinetics of FITC-PIP is greatly reduced, and the spreading behavior of the hexane solution is also impeded to some extent. Furthermore, in situ FT-IR spectroscopy demonstrates that by the mitigation of this PEI/TA interlayer, the interfacial polymerization process is greatly controlled. Moreover, the as-prepared NF membrane exhibits an increased water permeation flux of 65 L m^-2 h^-1 (at the operation pressure of 0.6 MPa), high Na₂SO₄ rejection of >99%, and excellent long-term structural stability.

Quantum Cascade Laser Infrared Spectroscopy for Online Monitoring of Hydroxylamine Nitrate

We describe a new approach for high sensitivity and real-time online measurements to monitor the kinetics in the processing of nuclear materials and other chemical reactions. Mid infrared (Mid-IR) quantum cascade laser (QCL) high-resolution spectroscopy was used for rapid and continuous sampling of nitrates in aqueous and organic reactive systems, using pattern recognition analysis and high sensitivity to detect and identify chemical species. In this standoff or off-set method, the collection of a sample for analysis is not required. To perform the analysis, a flow cell was used for in situ sampling of a liquid slipstream. A prototype was designed based on attenuated total reflection (ATR) coupled with the QCL beam to detect and identify chemical changes and be deployed in hostile environments, either radiological or chemical. The limit of detection (LOD) and the limit of quantification (LOQ) at 3σ for hydroxylamine nitrate ranged from 0.3 to 3 and from 3.5 to 10 g·L⁻¹, respectively, for the nitrate system at three peaks with wavelengths between 3.8 and 9.8 μm.

Application of FT-IR spectroscopy on breast cancer serum analysis

Breast cancer is regarded as the most malignant tumor among women throughout the world. Therefore, early detection and proper diagnostic methods have been known to help save women's lives. Fourier Transform Infrared (FT-IR) spectroscopy, coupled with PCA-LDA analysis, is a new technique to investigate the characteristics of serum in breast cancer. In this study, 43 breast cancer and 43 healthy serum samples were collected, and the FT-IR spectra were recorded for each one. Then, PCA analysis and linear discriminant analysis (LDA) were used to analyze the spectral data. The results showed that there were differences between the spectra of the two groups. Discriminating wavenumbers were associated with several spectral differences over the 950-1200cm^-1(sugar), 1190-1350cm^-1 (collagen), 1475-1710cm^-1 (protein), 1710-1760cm^-1 (ester), 2800-3000cm^-1 (stretching motions of -CH₂ & -CH₃), and 3090-3700cm^-1 (NH stretching) regions. PCA-LDA performance on serum IR could recognize changes between the control and the breast cancer cases. The diagnostic accuracy, sensitivity, and specificity of PCA-LDA analysis for 3000-3600cm^-1 (NH stretching) were found to be 83%, 84%, 74% for the control and 80%, 76%, 72% for the breast cancer cases, respectively. The results showed that the major spectral differences between the two groups were related to the differences in protein conformation in serum samples. It can be concluded that FT-IR spectroscopy, together with multivariate data analysis, is able to discriminate between breast cancer and healthy serum samples.

FTIR spectroscopy as a unified method for simultaneous analysis of intra- and extracellular metabolites in high-throughput screening of microbial bioprocesses

BACKGROUND

Analyses of substrate and metabolites are often bottleneck activities in high-throughput screening of microbial bioprocesses. We have assessed Fourier transform infrared spectroscopy (FTIR), in combination with high throughput micro-bioreactors and multivariate statistical analyses, for analysis of metabolites in high-throughput screening of microbial bioprocesses. In our previous study, we have demonstrated that high-throughput (HTS) FTIR can be used for estimating content and composition of intracellular metabolites, namely triglyceride accumulation in oleaginous filamentous fungi. As a continuation of that research, in the present study HTS FTIR was evaluated as a unified method for simultaneous quantification of intra- and extracellular metabolites and substrate consumption. As a proof of concept, a high-throughput microcultivation of oleaginous filamentous fungi was conducted in order to monitor production of citric acid (extracellular metabolite) and triglyceride lipids (intracellular metabolites), as well as consumption of glucose in the cultivation medium.

RESULTS

HTS FTIR analyses of supernatant samples was compared with an attenuated total reflection (ATR) FTIR, which is an established method for bioprocess monitoring. Glucose and citric acid content of growth media was quantified by high performance liquid chromatography (HPLC). Partial least square regression (PLSR) between HPLC glucose and citric acid data and the corresponding FTIR spectral data was used to set up calibration models. PLSR results for HTS measurements were very similar to the results obtained with ATR methodology, with high coefficients of determination (0.91-0.98) and low error values (4.9-8.6%) for both glucose and citric acid estimates.

CONCLUSIONS

The study has demonstrated that intra- and extracellular metabolites, as well as nutrients in the cultivation medium, can be monitored by a unified approach by HTS FTIR. The proof-of-concept study has validated that HTS FTIR, in combination with Duetz microtiter plate system and chemometrics, can be used for high throughput screening of microbial bioprocesses. It can be anticipated that the approach, demonstrated here on single-cell oil production by filamentous fungi, can find general application in screening studies of microbial bioprocesses, such as production of single-cell proteins, biopolymers, polysaccharides, carboxylic acids, and other type of metabolites.

Comparison of Fiber Optic and Conduit Attenuated Total Reflection (ATR) Fourier Transform Infrared (FT-IR) Setup for In-Line Fermentation Monitoring

The performance of a fiber optic and an optical conduit in-line attenuated total reflection mid-infrared (IR) probe during in situ monitoring of Penicillium chrysogenum fermentation were compared. The fiber optic probe was connected to a sealed, portable, Fourier transform infrared (FT-IR) process spectrometer via a plug-and-play interface. The optical conduit, on the other hand, was connected to a FT-IR process spectrometer via a knuckled probe with mirrors that had to be adjusted prior to each fermentation, which were purged with dry air. Penicillin V (PenV) and its precursor phenoxyacetic acid (POX) concentrations were determined by online high-performance liquid chromatography and the obtained concentrations were used as reference to build partial least squares regression models. Cross-validated root-mean-square errors of prediction were found to be 0.2 g L^-1 (POX) and 0.19 g L^-1 (PenV) for the fiber optic setup and 0.17 g L^-1 (both POX and PenV) for the conduit setup. Higher noise-levels and spectrum-to-spectrum variations of the fiber optic setup lead to higher noise of estimated (i.e., unknown) POX and PenV concentrations than was found for the conduit setup. It seems that trade-off has to be made between ease of handling (fiber optic setup) and measurement accuracy (optical conduit setup) when choosing one of these systems for bioprocess monitoring.

Advances in Mid-Infrared Spectroscopy for Chemical Analysis

Infrared spectroscopy in the 3-20 μm spectral window has evolved from a routine laboratory technique into a state-of-the-art spectroscopy and sensing tool by benefitting from recent progress in increasingly sophisticated spectra acquisition techniques and advanced materials for generating, guiding, and detecting mid-infrared (MIR) radiation. Today, MIR spectroscopy provides molecular information with trace to ultratrace sensitivity, fast data acquisition rates, and high spectral resolution catering to demanding applications in bioanalytics, for example, and to improved routine analysis. In addition to advances in miniaturized device technology without sacrificing analytical performance, selected innovative applications for MIR spectroscopy ranging from process analysis to biotechnology and medical diagnostics are highlighted in this review.