Rapid and non-invasive detection of malaria parasites using near-infrared spectroscopy and machine learning

BACKGROUND

Novel and highly sensitive point-of-care malaria diagnostic and surveillance tools that are rapid and affordable are urgently needed to support malaria control and elimination.

METHODS

We demonstrated the potential of near-infrared spectroscopy (NIRS) technique to detect malaria parasites both, in vitro, using dilutions of infected red blood cells obtained from Plasmodium falciparum cultures and in vivo, in mice infected with P. berghei using blood spotted on slides and non-invasively, by simply scanning various body areas (e.g., feet, groin and ears). The spectra were analysed using machine learning to develop predictive models for infection.

FINDINGS

Using NIRS spectra of in vitro cultures and machine learning algorithms, we successfully detected low densities (<10-7 parasites/μL) of P. falciparum parasites with a sensitivity of 96% (n = 1041), a specificity of 93% (n = 130) and an accuracy of 96% (n = 1171) and differentiated ring, trophozoite and schizont stages with an accuracy of 98% (n = 820). Furthermore, when the feet of mice infected with P. berghei with parasitaemia ≥3% were scanned non-invasively, the sensitivity and specificity of NIRS were 94% (n = 66) and 86% (n = 342), respectively.

INTERPRETATION

These data highlights the potential of NIRS technique as rapid, non-invasive and affordable tool for surveillance of malaria cases. Further work to determine the potential of NIRS to detect malaria in symptomatic and asymptomatic malaria cases in the field is recommended including its capacity to guide current malaria elimination strategies.

Soluble meso and deuteroporphyrin analogs of the malaria pigment hematin anhydride

Two soluble heme analogs of the insoluble malaria pigment hematin anhydride (HA, or β-hematin), [Fe(III)(protoporphyrin)]2, with either mesoporphyrin (MHA) or deuteroporphyrin (DHA) are characterized by elemental analysis, SEM, IR spectroscopy, electronic spectroscopy, paramagnetic 1H NMR spectroscopy and solution magnetic susceptibility. While prior single crystal and X-ray powder diffraction results indicate all three have a common propionate linked dimer motif, there is considerable solid state variation in the conformation. This is associated with enhanced solubility of MHA and DHA. As with HA, DHA undergoes thermally promoted reversible hydration/dehydration in the solid state. Solution 1H NMR studies of DHA suggest a high spin dimeric structure with the porphyrin methyls distributed between two isomers which are also present in the solid state. These soluble iron(III)porphyrin dimers allow for the first direct solution studies by NMR and UV-Vis spectroscopies of these key species. Taken together the results illustrate the importance and utility of varying the substituents on the periphery of the porphyrin for studying heme aggregation and malaria pigment formation.

Spectrally Resolved and Highly Parallelized Raman Difference Spectroscopy for the Analysis of Drug-Target Interactions between the Antimalarial Drug Chloroquine and Hematin

Malaria is a severe disease caused by cytozoic parasites of the genus Plasmodium, which infiltrate and infect red blood cells. Several drugs have been developed to combat the devastating effects of malaria. Antimalarials based on quinolines inhibit the crystallization of hematin into hemozoin within the parasite, ultimately leading to its demise. Despite the frequent use of these agents, there are unanswered questions about their mechanisms of action. In the present study, the quinoline chloroquine and its interaction with the target structure hematin was investigated using an advanced, highly parallelized Raman difference spectroscopy (RDS) setup. Simultaneous recording of the spectra of hematin and chloroquine mixtures with varying compositions enabled the observation of changes in peak heights and positions based on the altered molecular structure resulting from their interaction. A shift of (-1.12 ± 0.05) cm-1 was observed in the core-size marker band ν(CαCm)asym peak position of the 1:1 chloroquine-hematin mixture compared to pure hematin. The oxidation-state marker band ν(pyrrole half-ring)sym exhibited a shift by (+0.93 ± 0.13) cm-1. These results were supported by density functional theory (DFT) calculations, indicating a hydrogen bond between the quinolinyl moiety of chloroquine and the oxygen atom of ferric protoporphyrin IX hydroxide (Fe(III)PPIX-OH). The consequence is a reduced electron density within the porphyrin moiety and an increase in its core size. This hypothesis provided further insights into the mechanism of hemozoin inhibition, suggesting chloroquine binding to the monomeric form of hematin, thereby preventing its further crystallization to hemozoin.

Molecular Interactions Identified by Two-Dimensional Analysis-Detailed Insight into the Molecular Interactions of the Antimalarial Artesunate with the Target Structure β-Hematin by Means of 2D Raman Correlation Spectroscopy

A thorough understanding of the interaction of endoperoxide antimalarial agents with their biological target structures is of utmost importance for the tailored design of future efficient antimalarials. Detailed insights into molecular interactions between artesunate and β-hematin were derived with a combination of resonance Raman spectroscopy, two-dimensional correlation analysis, and density functional theory calculations. Resonance Raman spectroscopy with three distinct laser wavelengths enabled the specific excitation of different chromophore parts of β-hematin. The resonance Raman spectra of the artesunate-β-hematin complexes were thoroughly analyzed with the help of high-resolution and highly sensitive two-dimensional correlation spectroscopy. Spectral changes in the peak properties were found with increasing artesunate concentration. Changes in the low-frequency, morphology-sensitive Raman bands indicated a loss in crystallinity of the drug-target complexes. Differences in the high-wavenumber region were assigned to increased distortions of the planarity of the structure of the target molecule due to the appearance of various coexisting alkylation species. Evidence for the appearance of high-valent ferryl-oxo species could be observed with the help of differences in the peak properties of oxidation-state sensitive Raman modes. To support those findings, the relaxed ground-state structures of ten possible covalent mono- and di-meso(Cm)-alkylated hematin-dihydroartemisinyl complexes were calculated using density functional theory. A very good agreement with the experimental peak properties was achieved, and the out-of-plane displacements along the lowest-frequency normal coordinates were investigated by normal coordinate structural decomposition analysis. The strongest changes in all data were observed in vibrations with a high participation of Cm-parts of β-hematin.

Investigations on the Novel Antimalarial Ferroquine in Biomimetic Solutions Using Deep UV Resonance Raman Spectroscopy and Density Functional Theory

Deep ultraviolet (DUV) resonance Raman experiments are performed, investigating the novel, promising antimalarial ferroquine (FQ). Two buffered aqueous solutions with pH values of 5.13 and 7.00 are used, simulating the acidic and neutral conditions inside a parasite's digestive vacuole and cytosol, respectively. To imitate the different polarities of the membranes and interior, the buffer's 1,4-dioxane content was increased. These experimental conditions should mimic the transport of the drug inside malaria-infected erythrocytes through parasitophorous membranes. Supporting density functional theory (DFT) calculations on the drug's micro-speciation were performed, which could be nicely assigned to shifts in the peak positions of resonantly enhanced high-wavenumber Raman signals at λ_exc = 257 nm. FQ is fully protonated in polar mixtures like the host interior and the parasite's cytoplasm or digestive vacuole (DV) and is only present as a free base in nonpolar ones, such as the host's and parasitophorous membranes. Additionally, the limit of detection (LoD) of FQ at vacuolic pH values was determined using DUV excitation wavelengths at 244 and 257 nm. By applying the resonant laser line at λ_exc = 257 nm, a minimal FQ concentration of 3.1 μM was detected, whereas the pre-resonant excitation wavelength 244 nm provides an LoD of 6.9 μM. These values were all up to one order of magnitude lower than the concentration found for the food vacuole of a parasitized erythrocyte.

Discriminant Analysis PCA-LDA Assisted Surface-Enhanced Raman Spectroscopy for Direct Identification of Malaria-Infected Red Blood Cells

Various methods for detecting malaria have been developed in recent years, each with its own set of advantages. These methods include microscopic, antigen-based, and molecular-based analysis of blood samples. This study aimed to develop a new, alternative procedure for clinical use by using a large data set of surface-enhanced Raman spectra to distinguish normal and infected red blood cells. PCA-LDA algorithms were used to produce models for separating P. falciparum (3D7)-infected red blood cells and normal red blood cells based on their Raman spectra. Both average normalized spectra and spectral imaging were considered. However, these initial spectra could hardly differentiate normal cells from the infected cells. Then, discrimination analysis was applied to assist in the classification and visualization of the different spectral data sets. The results showed a clear separation in the PCA-LDA coordinate. A blind test was also carried out to evaluate the efficiency of the PCA-LDA separation model and achieved a prediction accuracy of up to 80%. Considering that the PCA-LDA separation accuracy will improve when a larger set of training data is incorporated into the existing database, the proposed method could be highly effective for the identification of malaria-infected red blood cells.

Visible microspectrophotometry coupled with machine learning to discriminate the erythrocytic life cycle stages of P. falciparum malaria parasites in functional single cells

Visible microspectroscopy combined with machine learning is able to detect and quantify functional malaria infected erythrocytes at different stages of the P. falciparum erythrocytic life cycle.

The Future in Sensing Technologies for Malaria Surveillance: A Review of Hemozoin-Based Diagnosis

Early and effective malaria diagnosis is vital to control the disease spread and to prevent the emergence of severe cases and death. Currently, malaria diagnosis relies on optical microscopy and immuno-rapid tests; however, these require a drop of blood, are time-consuming, or are not specific and sensitive enough for reliable detection of low-level parasitaemia. Thus, there is an urge for simpler, prompt, and accurate alternative diagnostic methods. Particularly, hemozoin has been increasingly recognized as an attractive biomarker for malaria detection. As the disease proliferates, parasites digest host hemoglobin, in the process releasing toxic haem that is detoxified into an insoluble crystal, the hemozoin, which accumulates along with infection progression. Given its magnetic, optical, and acoustic unique features, hemozoin has been explored for new label-free diagnostic methods. Thereby, herein, we review the hemozoin-based malaria detection methods and critically discuss their challenges and potential for the development of an ideal diagnostic device.

Ultraviolet/Visible and Near-Infrared Dual Spectroscopic Method for Detection and Quantification of Low-Level Malaria Parasitemia in Whole Blood

The scourge of malaria infection continues to strike hardest against pregnant women and children in Africa and South East Asia. For global elimination, testing methods that are ultrasensitive to low-level ring-staged parasitemia are urgently required. In this study, we used a novel approach for diagnosis of malaria infection by combining both electronic ultraviolet-visible (UV/vis) spectroscopy and near infrared (NIR) spectroscopy to detect and quantify low-level (1-0.000001%) ring-staged malaria-infected whole blood under physiological conditions uisng Multiclass classification using logistic regression, which showed that the best results were achieved using the extended wavelength range, providing an accuracy of 100% for most parasitemia classes. Likewise, partial least-squares regression (PLS-R) analysis showed a higher quantification sensitivity (R² = 0.898) for the extended spectral region compared to UV/vis and NIR (R² = 0.806 and 0.556, respectively). For quantifying different-stage blood parasites, the extended wavelength range was able to detect and quantify all thePlasmodium falciparum accurately compared to testing each spectral component separately. These results demonstrate the potential of a combined UV/vis-NIR spectroscopy to accurately diagnose malaria-infected patients without the need for elaborate sample preparation associated with the existing mid-IR approaches.

Quantitative diffuse optical spectroscopy for noninvasive measurements of the malaria pigment hemozoin

Hemozoin (Hz) is a crystal by-product of hemoglobin consumption by malaria parasites. There are currently no in vivo deep tissue sensing methods that can quantify Hz presence noninvasively, which would be advantageous for malaria research and treatment. In this work, we describe the broadband near-infrared optical characterization of synthetic Hz in static and dynamic tissue-simulating phantoms. Using hybrid frequency domain and continuous-wave near-infrared spectroscopy, we quantified the broadband optical absorption and scattering spectra of Hz and identified the presence of Hz at a minimum tissue-equivalent concentration of 0.014 µg/mL in static lipid emulsion phantoms simulating human adipose. We then constructed a whole blood-containing tissue-simulating phantom and demonstrated the detection of Hz at physiologically-relevant tissue oxygen saturations ranging from 70-90%. Our results suggest that quantitative diffuse optical spectroscopy may be useful for detecting deep tissue Hz in vivo.

Detection of malaria parasites in dried human blood spots using mid-infrared spectroscopy and logistic regression analysis

BACKGROUND

Epidemiological surveys of malaria currently rely on microscopy, polymerase chain reaction assays (PCR) or rapid diagnostic test kits for Plasmodium infections (RDTs). This study investigated whether mid-infrared (MIR) spectroscopy coupled with supervised machine learning could constitute an alternative method for rapid malaria screening, directly from dried human blood spots.

METHODS

Filter papers containing dried blood spots (DBS) were obtained from a cross-sectional malaria survey in 12 wards in southeastern Tanzania in 2018/19. The DBS were scanned using attenuated total reflection-Fourier Transform Infrared (ATR-FTIR) spectrometer to obtain high-resolution MIR spectra in the range 4000 cm-1 to 500 cm-1. The spectra were cleaned to compensate for atmospheric water vapour and CO2 interference bands and used to train different classification algorithms to distinguish between malaria-positive and malaria-negative DBS papers based on PCR test results as reference. The analysis considered 296 individuals, including 123 PCR-confirmed malaria positives and 173 negatives. Model training was done using 80% of the dataset, after which the best-fitting model was optimized by bootstrapping of 80/20 train/test-stratified splits. The trained models were evaluated by predicting Plasmodium falciparum positivity in the 20% validation set of DBS.

RESULTS

Logistic regression was the best-performing model. Considering PCR as reference, the models attained overall accuracies of 92% for predicting P. falciparum infections (specificity = 91.7%; sensitivity = 92.8%) and 85% for predicting mixed infections of P. falciparum and Plasmodium ovale (specificity = 85%, sensitivity = 85%) in the field-collected specimen.

CONCLUSION

These results demonstrate that mid-infrared spectroscopy coupled with supervised machine learning (MIR-ML) could be used to screen for malaria parasites in human DBS. The approach could have potential for rapid and high-throughput screening of Plasmodium in both non-clinical settings (e.g., field surveys) and clinical settings (diagnosis to aid case management). However, before the approach can be used, we need additional field validation in other study sites with different parasite populations, and in-depth evaluation of the biological basis of the MIR signals. Improving the classification algorithms, and model training on larger datasets could also improve specificity and sensitivity. The MIR-ML spectroscopy system is physically robust, low-cost, and requires minimum maintenance.

Recent Advancement in the Surface-Enhanced Raman Spectroscopy-Based Biosensors for Infectious Disease Diagnosis

Diagnosis is the key component in disease elimination to improve global health. However, there is a tremendous need for diagnostic innovation for neglected tropical diseases that largely consist of mosquito-borne infections and bacterial infections. Early diagnosis of these infectious diseases is critical but challenging because the biomarkers are present at low concentrations, demanding bioanalytical techniques that can deliver high sensitivity with ensured specificity. Owing to the plasmonic nanomaterials-enabled high detection sensitivities, even up to single molecules, surface-enhanced Raman spectroscopy (SERS) has gained attention as an optical analytical tool for early disease biomarker detection. In this mini-review, we highlight the SERS-based assay development tailored to detect key types of biomarkers for mosquito-borne and bacterial infections. We discuss in detail the variations of SERS-based techniques that have developed to afford qualitative and quantitative disease biomarker detection in a more accurate, affordable, and field-transferable manner. Current and emerging challenges in the advancement of SERS-based technologies from the proof-of-concept phase to the point-of-care phase are also briefly discussed.

Development of a label-free Raman imaging technique for differentiation of malaria parasite infected from non-infected tissue

During malarial infection, the host uses the spleen to clear the malaria parasites, however, the parasites have evolved the ability to bind to endothelial receptors in blood vessels of tissues to avoid removal, known as sequestration, and this is largely responsible for the symptoms and severity of infection. So a technique which could non-invasively diagnose tissue burden could be utilised as an aid for localised malaria diagnosis within tissue. Raman spectroscopy is a label-free imaging technique and can provide unique and chemically specific Raman 'fingerprint' spectrum of biological samples such as tissue. Within this study, Raman imaging was used to observe the changes to the molecular composition of mice spleen tissue under malarial infection, compared with non-infected samples. From analysis of the Raman imaging data, both tissue types showed very similar spectral profiles, which highlighted that their biochemical compositions were closely linked. Principal component analysis showed very clear separation of the two sample groups, with an associated increase in concentration of heme-based Raman vibrations within the infected dataset. This was indicative of the presence of hemozoin, the malaria pigment, being detected within the infected spleen. Separation also showed that as the hemozoin content within the tissue increased, there was a corresponding change to hemoglobin and some lipid/nucleic acid vibrations. These results demonstrate that Raman spectroscopy can be used to easily discriminate the subtle changes in tissue burden upon malarial infection.

Fiber enhanced Raman spectroscopic analysis as a novel method for diagnosis and monitoring of diseases related to hyperbilirubinemia and hyperbiliverdinemia

Fiber enhanced resonance Raman spectroscopy (FERS) is introduced for chemically selective and ultrasensitive analysis of the biomolecules hematin, hemoglobin, biliverdin, and bilirubin. The abilities for analyzing whole intact, oxygenated erythrocytes are proven, demonstrating the potential for the diagnosis of red blood cell related diseases, such as different types of anemia and hemolytic disorders. The optical fiber enables an efficient light-guiding within a miniaturized sample volume of only a few micro-liters and provides a tremendously improved analytical sensitivity (LODs of 0.5 μM for bilirubin and 0.13 μM for biliverdin with proposed improvements down to the pico-molar range). FERS is a less invasive method than the standard ones and could be a new analytical method for monitoring neonatal jaundice, allowing a precise control of the unconjugated serum bilirubin levels, and therefore, providing a better prognosis for newborns. The potential for sensing very low concentrations of the bile pigments may also open up new opportunities for cancer research. The abilities of FERS as a diagnostic tool are explored for the elucidation of jaundice with different etiologies including the rare, not yet well understood diseases manifested in green jaundice. This is demonstrated by quantifying clinically relevant concentrations of bilirubin and biliverdin simultaneously in the micro-molar range: for the case of hyperbilirubinemia due to malignancy, infectious hepatitis, cirrhosis or stenosis of the common bile duct (1 μM biliverdin together with 50 μM bilirubin) and for hyperbiliverdinemia (25 μM biliverdin and 75 μM bilirubin). FERS has high potential as an ultrasensitive analytical technique for a wide range of biomolecules and in various life-science applications.

Ultrasensitive Detection of Antiseptic Antibiotics in Aqueous Media and Human Urine Using Deep UV Resonance Raman Spectroscopy

Deep UV resonance Raman spectroscopy is introduced as an analytical tool for ultrasensitive analysis of antibiotics used for empirical treatment of patients with sepsis and septic shock, that is, moxifloxacin, meropenem, and piperacillin in aqueous solution and human urine. By employing the resonant excitation wavelengths λ_exc = 244 nm and λ_exc = 257 nm, only a small sample volume and short acquisition times are needed. For a better characterization of the matrix urine, the main ingredients were investigated. The capability of detecting the antibiotics in clinically relevant concentrations in aqueous media (LODs: 13.0 ± 1.4 μM for moxifloxacin, 43.6 ± 10.7 μM for meropenem, and 7.1 ± 0.6 μM for piperacillin) and in urine (LODs: 36.6 ± 11.0 μM for moxifloxacin, and 114.8 ± 3.1 μM for piperacillin) points toward the potential of UV Raman spectroscopy as point-of-care method for therapeutic drug monitoring (TDM). This procedure enables physicians to achieve fast adequate dosing of antibiotics to improve the outcome of patients with sepsis.

Raman Spectroscopy of Blood and Blood Components

Blood is a bodily fluid that is vital for a number of life functions in animals. To a first approximation, blood is a mildly alkaline aqueous fluid (plasma) in which a large number of free-floating red cells (erythrocytes), white cells (leucocytes), and platelets are suspended. The primary function of blood is to transport oxygen from the lungs to all the cells of the body and move carbon dioxide in the return direction after it is produced by the cells' metabolism. Blood also carries nutrients to the cells and brings waste products to the liver and kidneys. Measured levels of oxygen, nutrients, waste, and electrolytes in blood are often used for clinical assessment of human health. Raman spectroscopy is a non-destructive analytical technique that uses the inelastic scattering of light to provide information on chemical composition, and hence has a potential role in this clinical assessment process. Raman spectroscopic probing of blood components and of whole blood has been on-going for more than four decades and has proven useful in applications ranging from the understanding of hemoglobin oxygenation, to the discrimination of cancerous cells from healthy lymphocytes, and the forensic investigation of crime scenes. In this paper, we review the literature in the field, collate the published Raman spectroscopy studies of erythrocytes, leucocytes, platelets, plasma, and whole blood, and attempt to draw general conclusions on the state of the field.

Vibrational spectroscopic characterization of arylisoquinolines by means of Raman spectroscopy and density functional theory calculations

Seven new AIQ antimalarial agents were investigated using FT-NIR and deep-UV resonance Raman spectroscopy.

Optofluidic single-cell absorption flow analyzer for point-of-care diagnosis of malaria

In this work, an optofluidic flow analyzer, which can be used to perform malaria diagnosis at the point-of-care is demonstrated. The presented technique is based on quantitative optical absorption measurements carried out on a single cell level for a given population of Human Red Blood Cells (RBCs). By measuring the optical absorption of each RBC, the decrease in the Hemoglobin (Hb) concentration in the cytoplasm of the cell due to the invasion of malarial parasite is detected. Cells are assessed on a single cell basis, as they pass through a microfluidic channel. The proposed technique has been implemented with inexpensive off-the-shelf components like laser diode, photo-detector and a micro-controller. The ability of the optofluidic flow analyzer to asses about 308,049 cells within 3 minutes has been demonstrated. The presented technique is capable of detecting very low parasitemia levels with high sensitivity.

Towards ultrasensitive malaria diagnosis using surface enhanced Raman spectroscopy

We report two methods of surface enhanced Raman spectroscopy (SERS) for hemozoin detection in malaria infected human blood. In the first method, silver nanoparticles were synthesized separately and then mixed with lysed blood; while in the second method, silver nanoparticles were synthesized directly inside the parasites of Plasmodium falciparum. It was observed that the first method yields a smaller variation in SERS measurements and stronger correlation between the estimated contribution of hemozoin and the parasitemia level, which is preferred for the quantification of the parasitemia level. In contrast, the second method yields a higher sensitivity to a low parasitemia level thus could be more effective in the early malaria diagnosis to determine whether a given blood sample is positive.

Label-free Raman imaging of the macrophage response to the malaria pigment hemozoin

Hemozoin, the 'malaria pigment', is engulfed by phagocytic cells, such as macrophages, during malaria infection. This biocrystalline substance is difficult to degrade and often accumulates in phagocytes. The macrophage response to hemozoin relates to the severity of the disease and the potential for malaria-related disease complications. In this study we have used Raman spectroscopy as a label-free method to investigate the biochemical changes occurring in macrophages during the first few hours of hemozoin uptake. We found a number of distinct spectral groups, spectrally or spatially related to the presence of the hemozoin inside the cell. Intracellular hemozoin was spectrally identical to extracellular hemozoin, regardless of the location in the cell. A small proportion of hemozoin was found to be associated with lipid-based components, consistent with the uptake of hemozoin into vesicles such as phagosomes and lysosomes. The spatial distribution of the hemozoin was observed to be inhomogeneous, and its presence largely excluded that of proteins and lipids, demonstrating that cells were not able to break down the biocrystals on the time scales studied here. These results show that Raman imaging can be used to answer some of the open questions regarding the role of hemozoin in the immune response. How different combinations of hemozoin and other molecules are treated by macrophages, whether hemozoin can be broken down by the cell, and more importantly, which co-factors or products are involved in the subsequent cell reaction are the expected issues to be elucidated by this technique.

In vivo microscopy of hemozoin: towards a needle free diagnostic for malaria

Clinical diagnosis of malaria suffers from poor specificity leading to overtreatment with antimalarial medications. Alternatives, like blood smear microscopy or antigen-based tests, require a blood sample. We investigate in vivo microscopy as a needle-free malaria diagnostic. Two optical signatures, birefringence and absorbance, of the endogenous malaria by-product hemozoin were evaluated as in vivo optical biomarkers. Hemozoin birefringence was difficult to detect in highly scattering tissue; however, hemozoin absorbance was observed in increasingly complex biological environments and detectable over a clinically-relevant range of parasitemia in vivo in a P. yoelii-infected mouse model of malaria.

Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes.

Enhanced Raman multigas sensing - a novel tool for control and analysis of (13)CO(2) labeling experiments in environmental research

Cavity-enhanced Raman multigas spectrometry is introduced as a versatile technique for monitoring of (13)CO2 isotope labeling experiments, while simultaneously quantifying the fluxes of O2 and other relevant gases across a wide range of concentrations. The multigas analysis was performed in a closed cycle; no gas was consumed, and the gas composition was not altered by the measurement. Isotope labeling of plant metabolites via photosynthetic uptake of (13)CO2 enables the investigation of resource flows in plants and is now an important tool in ecophysiological studies. In this experiment the (13)C labeling of monoclonal cuttings of Populus trichocarpa was undertaken. The high time resolution of the online multigas analysis allowed precise control of the pulse labeling and was exploited to calculate the kinetics of photosynthetic (13)CO2 uptake and to extrapolate the exact value of the (13)CO2 peak concentration in the labeling chamber. Further, the leaf dark respiration of immature and mature leaves was analyzed. The quantification of the photosynthetic O2 production rate as a byproduct of the (13)CO2 uptake correlated with the amount of available light and the leaf area of the plants in the labeling chamber. The ability to acquire CO2 and O2 respiration rates simultaneously also simplifies the determination of respiratory quotients (rate of O2 uptake compared to CO2 release) and thus indicates the type of combusted substrate. By combining quantification of respiration quotients with the tracing of (13)C in plants, cavity enhanced Raman spectroscopy adds a valuable new tool for studies of metabolism at the organismal to ecosystem scale.

Microbial respiration and natural attenuation of benzene contaminated soils investigated by cavity enhanced Raman multi-gas spectroscopy

Soil and groundwater contamination with benzene can cause serious environmental damage. However, many soil microorganisms are capable to adapt and are known to strongly control the fate of organic contamination. Innovative cavity enhanced Raman multi-gas spectroscopy (CERS) was applied to investigate the short-term response of the soil micro-flora to sudden surface contamination with benzene regarding the temporal variations of gas products and their exchange rates with the adjacent atmosphere. (13)C-labeled benzene was spiked on a silty-loamy soil column in order to track and separate the changes in heterotrophic soil respiration - involving (12)CO2 and O2- from the natural attenuation process of benzene degradation to ultimately form (13)CO2. The respiratory quotient (RQ) decreased from a value 0.98 to 0.46 directly after the spiking and increased again within 33 hours to a value of 0.72. This coincided with the maximum (13)CO2 concentration rate (0.63 μmol m(-2) s(-1)), indicating the highest benzene degradation at 33 hours after the spiking event. The diffusion of benzene in the headspace and the biodegradation into (13)CO2 were simultaneously monitored and 12 days after the benzene spiking no measurable degradation was detected anymore. The RQ finally returned to a value of 0.96 demonstrating the reestablished aerobic respiration.

Rapid monitoring of intermediate states and mass balance of nitrogen during denitrification by means of cavity enhanced Raman multi-gas sensing

The comprehensive investigation of changes in N cycling has been challenging so far due to difficulties with measuring gases such as N2 and N2O simultaneously. In this study we introduce cavity enhanced Raman gas spectroscopy as a new analytical methodology for tracing the stepwise reduction of (15)N-labelled nitrate by the denitrifying bacteria Pseudomonas stutzeri. The unique capabilities of Raman multi-gas analysis enabled real-time, continuous, and non-consumptive quantification of the relevant gases ((14)N2, (14)N2O, O2, and CO2) and to trace the fate of (15)N-labeled nitrate substrate ((15)N2, (15)N2O) added to a P. stutzeri culture with one single measurement. Using this new methodology, we could quantify the kinetics of the formation and degradation for all gaseous compounds (educts and products) and thus study the reaction orders. The gas quantification was complemented with the analysis of nitrate and nitrite concentrations for the online monitoring of the total nitrogen element budget. The simultaneous quantification of all gases also enabled the contactless and sterile online acquisition of the pH changes in the P. stutzeri culture by the stoichiometry of the redox reactions during denitrification and the CO2-bicarbonate equilibrium. Continuous pH monitoring - without the need to insert an electrode into solution - elucidated e.g. an increase in the slope of the pH value coinciding with an accumulation of nitrite, which in turn led to a temporary accumulation of N2O, due to an inhibition of nitrous oxide reductase. Cavity enhanced Raman gas spectroscopy has a high potential for the assessment of denitrification processes and can contribute substantially to our understanding of nitrogen cycling in both natural and agricultural systems.

Raman spectroscopic investigation of 13CO 2 labeling and leaf dark respiration of Fagus sylvatica L. (European beech)

An important issue, in times of climate change and more extreme weather events, is the investigation of forest ecosystem reactions to these events. Longer drought periods stress the vitality of trees and promote mass insect outbreaks, which strongly affect ecosystem processes and services. Cavity-enhanced Raman gas spectrometry was applied for online multi-gas analysis of the gas exchange rates of O2 and CO2 and the labeling of Fagus sylvatica L. (European beech) seedlings with (13)CO2. The rapid monitoring of all these gases simultaneously allowed for the separation of photosynthetic uptake of CO2 by the beech seedlings and a constant (12)CO2 efflux via respiration and thus for a correction of the measured (12)CO2 concentrations in course of the labeling experiment. The effects of aphid infestation with the woolly beech aphid (Phyllaphis fagi L.) as well as the effect of a drought period on the respirational gas exchange were investigated. A slightly decreased respirational activity of drought-stressed seedlings in comparison to normally watered seedlings was found already for a low drought intensity. Cavity-enhanced Raman gas monitoring of O2, (12)CO2, and (13)CO2 was proven to be a powerful new tool for studying the effect of drought stress and aphid infestation on the respirational activity of European beech seedlings as an example of important forest species in Central Europe.

Online investigation of respiratory quotients in Pinus sylvestris and Picea abies during drought and shading by means of cavity-enhanced Raman multi-gas spectrometry

CERS monitoring of RQ values enables the analysis of nutrition shifts in trees in response to environmental stress.

Optimization of Fe3O4@Ag nanoshells in magnetic field-enriched surface-enhanced resonance Raman scattering for malaria diagnosis

The great potential of magnetic field enriched surface enhanced resonance Raman spectroscopy (SERRS) for early malaria diagnosis has been demonstrated previously. This technique is able to detect β-hematin, which is equivalent to a malaria biomarker (hemozoin) in Raman features, at a concentration of 5 nM. In this study, we present the optimization of nanoparticles used in the magnetic field enriched SERRS by tuning the core size and shell thickness of nanoparticles with an iron oxide core and a silver shell (Fe3O4@Ag). The discrete dipole approximation (DDA) model was introduced to investigate the localized electromagnetic field distributions and extinction efficiencies of the aggregate of Fe3O4@Ag and β-hematin, in correlation with their magnetic field enriched SERRS performance. We find that the optimal core-shell size of Fe3O4@Ag leading to the effective aggregation of Fe3O4@Ag and β-hematin under an external magnetic field with superior extinction efficiencies is the key to realize highly augmented Raman signals in this strategy. Furthermore, it is noted that the optimized result differs from the case without the external magnetic field to that with the external magnetic field. Therefore, this work demonstrates experimentally and theoretically the potential of tuning the core-shell Fe3O4@Ag for achieving the efficient magnetic field-enriched SERRS detection of β-hematin for early malaria diagnosis.

Double antiresonant hollow core fiber--guidance in the deep ultraviolet by modified tunneling leaky modes

Guiding light inside the hollow cores of microstructured optical fibers is a major research field within fiber optics. However, most of current fibers reveal limited spectral operation ranges between the mid-visible and the infrared and rely on complicated microstructures. Here we report on a new type of hollow-core fiber, showing for the first time distinct transmission windows between the deep ultraviolet and the near infrared. The fiber, guiding in a single mode, operates by the central core mode being anti-resonant to adjacent modes, leading to a novel modified tunneling leaky mode. The fiber design is straightforward to implement and reveals beneficial features such as preselecting the lowest loss mode (Gaussian-like or donut-shaped mode). Fibers with such a unique combination of attributes allow accessing the extremely important deep-UV range with Gaussian-like mode quality and may pave the way for new discoveries in biophotonics, multispectral spectroscopy, photo-initiated chemistry or ultrashort pulse delivery.

Fiber-enhanced Raman multigas spectroscopy: a versatile tool for environmental gas sensing and breath analysis

Versatile multigas analysis bears high potential for environmental sensing of climate relevant gases and noninvasive early stage diagnosis of disease states in human breath. In this contribution, a fiber-enhanced Raman spectroscopic (FERS) analysis of a suite of climate relevant atmospheric gases is presented, which allowed for reliable quantification of CH4, CO2, and N2O alongside N2 and O2 with just one single measurement. A highly improved analytical sensitivity was achieved, down to a sub-parts per million limit of detection with a high dynamic range of 6 orders of magnitude and within a second measurement time. The high potential of FERS for the detection of disease markers was demonstrated with the analysis of 27 nL of exhaled human breath. The natural isotopes (13)CO2 and (14)N(15)N were quantified at low levels, simultaneously with the major breath components N2, O2, and (12)CO2. The natural abundances of (13)CO2 and (14)N(15)N were experimentally quantified in very good agreement to theoretical values. A fiber adapter assembly and gas filling setup was designed for rapid and automated analysis of multigas compositions and their fluctuations within seconds and without the need for optical readjustment of the sensor arrangement. On the basis of the abilities of such miniaturized FERS system, we expect high potential for the diagnosis of clinically administered (13)C-labeled CO2 in human breath and also foresee high impact for disease detection via biologically vital nitrogen compounds.

Raman spectroscopic analysis of malaria disease progression via blood and plasma samples

In this study Raman spectroscopy has been used to monitor the changes in erythrocytes and plasma during Plasmodium infection in mice, following malaria disease progression over the course of 7 days. The Raman spectra of both samples are dominated by the spectra of hemoglobin and hemozoin, due to their resonant enhancement. In plasma samples, due to the inherently low heme background, heme-based changes in the Raman spectra could be detected in the very early stages of infection, as little as one day after Plasmodium infection, where parasitemia levels were low, on the order of 0.2%, and typically difficult to detect by existing methods. Further principal component analysis also indicates concurrent erythrocyte membrane changes at around day 4, where parasitemia levels reached 3%. These results show that plasma analysis has significant potential for early, quantitative and automated detection of malaria, and to quantify heme levels in serum which modulate malarial effects on the immune system.

Schistosoma mansoni hemozoin modulates alternative activation of macrophages via specific suppression of Retnla expression and secretion

The trematode Schistosoma mansoni is one of the etiological agents of schistosomiasis, a key neglected tropical disease responsible for an estimated annual loss of 70 million disability-adjusted life years. Hematophagy represents the primary nutrient acquisition pathway of this parasite, but digestion of hemoglobin also liberates toxic heme. Schistosomes detoxify heme via crystallization into hemozoin, which is subsequently regurgitated into the host's circulation. Here we demonstrate that during experimental schistosomiasis, hemozoin accumulating in the mouse liver is taken up by phagocytes at a time coincident with the development of the egg-induced T-helper 2 (Th2) granulomatous immune response. Furthermore, the uptake of hemozoin also coincides with the hepatic expression of markers of alternative macrophage activation. Alternatively activated macrophages are a key effector cell population associated with protection against schistosomiasis, making hemozoin well placed to play an important immunomodulatory role in this disease. To systematically explore this hypothesis, S. mansoni hemozoin was purified and added to in vitro bone marrow-derived macrophage cultures concurrently exposed to cytokines chosen to reflect the shifting state of macrophage activation in vivo. Macrophages undergoing interleukin-4 (IL-4)-induced alternative activation in the presence of hemozoin developed a phenotype specifically lacking in Retnla, a characteristic alternatively activated macrophage product associated with regulation of Th2 inflammatory responses. As such, in addition to its important detoxification role during hematophagy, we propose that schistosome hemozoin also provides a potent immunomodulatory function in the coevolved network of host-parasite relationships during schistosomiasis.

Tip-enhanced Raman scattering (TERS) from hemozoin crystals within a sectioned erythrocyte

Tip-enhanced Raman scattering (TERS) is a powerful technique to obtain molecular information on a nanometer scale, however, the technique has been limited to cell surfaces, viruses, and isolated molecules. Here we show that TERS can be used to probe hemozoin crystals at less than 20 nm spatial resolution in the digestive vacuole of a sectioned malaria parasite-infected cell. The TERS spectra clearly show characteristic bands of hemozoin that can be correlated to a precise position on the crystal by comparison with the corresponding atomic force microscopy (AFM) image. These are the first recorded AFM images of hemozoin crystals inside malaria-infected cells and clearly show the hemozoin crystals protruding from the embedding medium. TERS spectra recorded of these crystals show spectral features consistent with a five-coordinate high-spin ferric heme complex, which include the electron density marker band ν(4) at 1373 cm(-1) and other porphyrin skeletal and ring breathing modes at approximately 1636, 1557, 1412, 1314, 1123, and 1066 cm(-1). These results demonstrate the potential of the AFM/TERS technique to obtain nanoscale molecular information within a sectioned single cell. We foresee this approach paving the way to a new independent drug screening modality for detection of drugs binding to the hemozoin surface within the digestive vacuole of the malaria trophozoite.

Structural analysis of the antimalarial drug halofantrine by means of Raman spectroscopy and density functional theory calculations

The structure of the antimalarial drug halofantrine is analyzed by means of density functional theory (DFT) calculations, IR, and Raman spectroscopy. Strong, selective enhancements of the Raman bands of halofantrine at 1621 and 1590 cm(-1) are discovered by means of UV resonance Raman spectroscopy with excitation wavelength lambda(exc)=244 nm. These signal enhancements can be exploited for a localization of small concentrations of halofantrine in a biological environment. The Raman spectrum of halofantrine is calculated by means of DFT calculations [B3LYP/6-311+G(d,p)]. The calculation is very useful for a thorough mode assignment of the Raman bands of halofantrine. The strong bands at 1621 and 1590 cm(-1) in the UV Raman spectrum are assigned to combined C[Double Bond]C stretching vibrations in the phenanthrene ring of halofantrine. These bands are considered as putative marker bands for pipi interactions with the biological target molecules. The calculation of the electron density demonstrates a strong distribution across the phenanthrene ring of halofantrine, besides the electron withdrawing effect of the Cl and CF(3) substituents. This strong and even electron density distribution supports the hypothesis of pipi stacking as a possible mode of action of halofantrine. Complementary IR spectroscopy is performed for an investigation of vibrations of polar functional groups of the halofantrine molecule.