Raman properties of chlorophyll d, the major pigment of Acaryochloris marina: studies using both Raman spectroscopy and density functional theory

Unlocking Cd(II) biosorption potential of Candida tropicalis XTA 1874 for sustainable wastewater treatment

Cd(II) is a potentially toxic heavy metal having carcinogenic activity. It is becoming widespread in the soil and groundwater by various natural and anthropological activities. This is inviting its immediate removal. The present study is aimed at developing a Cd(II) resistant strain isolated from contaminated water body and testing its potency in biological remediation of Cd(II) from aqueous environment. The developed resistant strain was characterized by SEM, FESEM, TEM, EDAX, FT-IR, Raman Spectral, XRD and XPS analysis. The results depict considerable morphological changes had taken place on the cell surface and interaction of Cd(II) with the surface exposed functional groups along with intracellular accumulation. Molecular contribution of critical cell wall component has been evaluated. The developed resistant strain had undergone Cd(II) biosorption study by employing adsorption isotherms and kinetic modeling. Langmuir model best fitted the Cd(II) biosorption data compared to the Freundlich one. Cd(II) biosorption by the strain followed a pseudo second order kinetics. The physical parameters affecting biosorption were also optimized by employing response surface methodology using central composite design. The results depict remarkable removal capacity 75.682 ± 0.002% of Cd(II) by the developed resistant strain from contaminated aqueous medium using 500 ppm of Cd(II). Quantitatively, biosorption for Cd(II) by the newly developed resistant strain has been increased significantly (p < 0.0001) from 4.36 ppm (non-resistant strain) to 378.41 ppm (resistant strain). It has also shown quite effective desorption capacity 87.527 ± 0.023% at the first desorption cycle and can be reused effectively as a successful Cd(II) desorbent up to five cycles. The results suggest that the strain has considerable withstanding capacity of Cd(II) stress and can be employed effectively in the Cd(II) bioremediation from wastewater.

Good vibrations: Raman spectroscopy enables insights into plant biochemical composition

Non-invasive techniques are needed to enable an integrated understanding of plant metabolic responses to environmental stresses. Raman spectroscopy is one such technique, allowing non-destructive chemical characterisation of samples in situ and in vivo and resolving the chemical composition of plant material at scales from microns to metres. Here, we review Raman band assignments of pigments, structural and non-structural carbohydrates, lipids, proteins and secondary metabolites in plant material and consider opportunities this technology raises for studies in vascular plant physiology.

Raman Spectroscopy and Its Modifications Applied to Biological and Medical Research

Nowadays, there is an interest in biomedical and nanobiotechnological studies, such as studies on carotenoids as antioxidants and studies on molecular markers for cardiovascular, endocrine, and oncological diseases. Moreover, interest in industrial production of microalgal biomass for biofuels and bioproducts has stimulated studies on microalgal physiology and mechanisms of synthesis and accumulation of valuable biomolecules in algal cells. Biomolecules such as neutral lipids and carotenoids are being actively explored by the biotechnology community. Raman spectroscopy (RS) has become an important tool for researchers to understand biological processes at the cellular level in medicine and biotechnology. This review provides a brief analysis of existing studies on the application of RS for investigation of biological, medical, analytical, photosynthetic, and algal research, particularly to understand how the technique can be used for lipids, carotenoids, and cellular research. First, the review article shows the main applications of the modified Raman spectroscopy in medicine and biotechnology. Research works in the field of medicine and biotechnology are analysed in terms of showing the common connections of some studies as caretenoids and lipids. Second, this article summarises some of the recent advances in Raman microspectroscopy applications in areas related to microalgal detection. Strategies based on Raman spectroscopy provide potential for biochemical-composition analysis and imaging of living microalgal cells, in situ and in vivo. Finally, current approaches used in the papers presented show the advantages, perspectives, and other essential specifics of the method applied to plants and other species/objects.

Raman Spectroscopy and Machine-Learning for Early Detection of Bacterial Canker of Tomato: The Asymptomatic Disease Condition

Bacterial canker of tomato is caused by Clavibacter michiganensis subsp. michiganensis (Cmm). The disease is highly destructive, because it produces latent asymptomatic infections that favor contagion rates. The present research aims consisted on the implementation of Raman spectroscopy (RS) and machine-learning spectral analysis as a method for the early disease detection. Raman spectra were obtained from infected asymptomatic tomato plants (BCTo) and healthy controls (HTo) with 785 nm excitation laser micro-Raman spectrometer. Spectral data were normalized and processed by principal component analysis (PCA), then the classifiers algorithms multilayer perceptron (PCA + MLP) and linear discriminant analysis (PCA + LDA) were implemented. Bacterial isolation and identification (16S rRNA gene sequencing) were realized of each plant studied. The Raman spectra obtained from tomato leaf samples of HTo and BCTo exhibited peaks associated to cellular components, and the most prominent vibrational bands were assigned to carbohydrates, carotenoids, chlorophyll, and phenolic compounds. Biochemical changes were also detectable in the Raman spectral patterns. Raman bands associated with triterpenoids and flavonoids compounds can be considered as indicators of Cmm infection during the asymptomatic stage. RS is an efficient, fast and reliable technology to differentiate the tomato health condition (BCTo or HTo). The analytical method showed high performance values of sensitivity, specificity and accuracy, among others.

Excited State Frequencies of Chlorophyll f and Chlorophyll a and Evaluation of Displacement through Franck-Condon Progression Calculations

We present ground and excited state frequency calculations of the recently discovered extremely red-shifted chlorophyll f. We discuss the experimentally available vibrational mode assignments of chlorophyll f and chlorophyll a which are characterised by particularly large downshifts of 13¹-keto mode in the excited state. The accuracy of excited state frequencies and their displacements are evaluated by the construction of Franck–Condon (FC) and Herzberg–Teller (HT) progressions at the CAM-B3LYP/6-31G(d) level. Results show that while CAM-B3LYP results are improved relative to B3LYP calculations, the displacements and downshifts of high-frequency modes are underestimated still, and that the progressions calculated for low temperature are dominated by low-frequency modes rather than fingerprint modes that are Resonant Raman active.

Cross-Selectivity Enhancement of Poly(vinylidene fluoride-hexafluoropropylene)-Based Sensor Arrays for Detecting Acetone and Ethanol

Two methods for cross-selectivity enhancement of porous poly(vinylidene fluoride-hexafluoropropylene) (PVDF-HFP)/carbon black (CB) composite-based resistive sensors are provided. The sensors are tested with acetone and ethanol in the presence of humid air. Cross-selectivity is enhanced using two different methods to modify the basic response of the PVDF-HFP/CB sensing platform. In method I, the adsorption properties of PVDF-HFP/CB are altered by adding a polyethylene oxide (PEO) layer or by treating with infrared (IR). In method II, the effects of the interaction of acetone and ethanol are enhanced by adding diethylene carbonate (DEC) or PEO dispersed in DEC (PEO/DEC) to the film. The results suggest the approaches used in method I alter the composite ability to adsorb acetone and ethanol, while in method II, they alter the transduction characteristics of the composite. Using these approaches, sensor relative response to acetone was increased by 89% compared with the PVDF-HFP/CB untreated film, whereas sensor relative response to ethanol could be decreased by 57% or increased by 197%. Not only do these results demonstrate facile methods for increasing sensitivity of PVDF-HFP/CB film, used in parallel they demonstrate a roadmap for enhancing system cross-selectivity that can be applied to separate units on an array. Fabrication methods, experimental procedures and results are presented and discussed.

Raman activated cell sorting

Single cell Raman spectra (SCRS) are intrinsic biochemical profiles and 'chemical images' of single cells which can be used to characterise phenotypic changes, physiological states and functions of cells. On the base of SCRS, Raman activated cell sorting (RACS) provides a label-free cell sorting approach, which can link single cells to their chemical or phenotypic profiles. Overcoming naturally weak Raman signals, establishing Raman biomarker as sorting criteria to RACS and improving specific sorting technology are three challenges of developing RACS. Advances on Raman spectroscopy such as stimulated Raman scattering (SRS) and pre-screening helped to increase RACS sorting speed. Entire SCRS can be characterised using pattern recognition methods, and specific Raman bands can be extracted as biomarkers for RACS. Recent advances on cell sorting technologies based on microfluidic device and surface-ejection enable accurate and reliable single cell sorting from complex samples. A high throughput RACS will be achievable in near future by integrating fast Raman detection system such as SRS with microfluidic RACS and Raman activated cell ejection (RACE).

Effects of the central metal on stretching vibrational bands of the peripheral carbonyl moieties in formylated chlorophyll derivatives studied by Fourier-transform infrared spectroscopy

The vibrational properties of metal complexes of monoformylated and diformylated chlorophyll derivatives were compared with those of the corresponding free-base chlorins to unravel the effects of the central metal on the carbonyl stretching vibration modes of the peripheral oxygen functional groups in the chlorin macrocycle by means of FTIR spectroscopy. The 3- C = O stretching vibrational bands of a 3-formyl group were shifted to lower wavenumbers by insertion of Zn and Cu into the center of the 3-formyl free-base chlorin. In contrast, the 7- and 8- C = O stretching vibrational bands of the formyl groups linked to the B-ring of the chlorin macrocycle were barely shifted even if 7- and 8-formyl free-base chlorins were metalated. The down-shifts of the 3- C = O and few shifts of the 7-/8- C = O vibrational stretching bands were in line with the results of DFT calculations. The difference in the effects of the central metal on the vibrational properties between the formyl group in the A-ring and those in the B-ring is ascribable to the different conjugation manners with the adjacent π-system: the 3-formyl group was connected to the chlorin 18π-system, whereas the 7-/8-formyl groups were conjugated to the rather isolated C 7– C 8 double bond. The 13- C = O stretching vibrational bands were shifted to lower wavenumbers by metalation. These down-shifts can also be rationalized by invoking the conjugation of the 13-keto group with the chlorin 18π-system.

Phosphorescence study of chlorophyll d photophysics. Determination of the energy and lifetime of the photo-excited triplet state. Evidence of singlet oxygen photosensitization

Chlorophyll d (Chl d) is the major pigment in both photosystems (PSI and II) of the cyanobacterium Acaryochloris marina, whose pigment composition represents an interesting alternative in oxygenic photosynthesis. While abundant information is available relative to photophysical properties of Chl a , the understanding of Chl d photophysics is still incomplete. In this paper, we present for the first time a characterization of Chl d phosphorescence, which accompanies radiative deactivation of the photoexcited triplet state of this pigment. Reliable information was obtained on the energy and lifetime of the Chl d triplet state in frozen solutions at 77 K using diethyl ether and aqueous dispersions of Triton X100 as solvents. It is shown that triplet Chl d is effectively populated upon photoexcitation of pigment molecules and efficiently sensitizes singlet oxygen phosphorescence in aerobic solutions under ambient conditions. The data obtained are compared with the previous results of the phosphorescence studies of Chl a and Pheo a, and their possible biological implications are discussed.

Enzyme activation and catalysis: characterisation of the vibrational modes of substrate and product in protochlorophyllide oxidoreductase

The light-dependent reduction of protochlorophyllide, a key step in the synthesis of chlorophyll, is catalyzed by the enzyme protochlorophyllide oxidoreductase (POR) and requires two photons (O. A. Sytina et al., Nature, 2008, 456, 1001-1008). The first photon activates the enzyme-substrate complex, a subsequent second photon initiates the photochemistry by triggering the formation of a catalytic intermediate. These two events are characterized by different spectral changes in the infra-red spectral region. Here, we investigate the vibrational frequencies of the POR-bound and unbound substrate, and product, and thus provide a detailed assignment of the spectral changes in the 1800-1250 cm(-1) region associated with the catalytic conversion of PChlide:NADPH:TyrOH into Chlide:NADP(+):TyrO(-). Fluorescence line narrowed spectra of the POR-bound Pchlide reveal a C=O keto group downshifted by more than 20 cm(-1) to a relatively low vibrational frequency of 1653 cm(-1), as compared to the unbound Pchlide, indicating that binding of the chromophore to the protein occurs via strong hydrogen bond(s). The frequencies of the C=C vibrational modes are consistent with a six-coordinated state of the POR-bound Pchlide, suggesting that there are two coordination interactions between the central Mg atom of the chromophore and protein residues, and/or a water molecule. The frequencies of the C=C vibrational modes of Chlide are consistent with a five-coordinated state, indicating a single interaction between the central Mg atom of the chromophore and a water molecule. Rapid-scan FTIR measurements on the Pchlide:POR:NADPH complex at 4 cm(-1) spectral resolution reveal a new band in the 1670 cm(-1) region. The FTIR spectra of the enzyme activation phase indicate involvement of a nucleotide-binding structural motif, and an increased exposure of the protein to solvent after activation.

Raman spectroscopy analysis of botryococcene hydrocarbons from the green microalga Botryococcus braunii

Botryococcus braunii, B race is a unique green microalga that produces large amounts of liquid hydrocarbons known as botryococcenes that can be used as a fuel for internal combustion engines. The simplest botryococcene (C(30)) is metabolized by methylation to give intermediates of C(31), C(32), C(33), and C(34), with C(34) being the predominant botryococcene in some strains. In the present work we have used Raman spectroscopy to characterize the structure of botryococcenes in an attempt to identify and localize botryococcenes within B. braunii cells. The spectral region from 1600-1700 cm(-1) showed ν(C=C) stretching bands specific for botryococcenes. Distinct botryococcene Raman bands at 1640 and 1647 cm(-1) were assigned to the stretching of the C=C bond in the botryococcene branch and the exomethylene C=C bonds produced by the methylations, respectively. A Raman band at 1670 cm(-1) was assigned to the backbone C=C bond stretching. Density function theory calculations were used to determine the Raman spectra of all botryococcenes to compare computed theoretical values with those observed. The analysis showed that the ν(C=C) stretching bands at 1647 and 1670 cm(-1) are actually composed of several closely spaced bands arising from the six individual C=C bonds in the molecule. We also used confocal Raman microspectroscopy to map the presence and location of methylated botryococcenes within a colony of B. braunii cells based on the methylation-specific 1647 cm(-1) botryococcene Raman shift.

Vibrational mode frequency calculations of chlorophyll-d for assessing (P740(+)-P740) FTIR difference spectra obtained using photosystem I particles from Acaryochloris marina

Acaryochloris marina is an oxygen-evolving organism that utilizes chlorophyll-d for light induced photochemistry. In photosystem I particles from Acaryochloris marina, the primary electron donor is called P740, and it is thought that P740 consist of two chlorophyll-d molecules. (P740(+)-P740) FTIR difference spectra have been produced, and vibrational features that are specific to chlorophyll-d (and not chlorophyll-a) were observed, supporting the idea that P740 consists chlorophyll-d molecules. Although bands in the (P740(+)-P740) FTIR difference spectra were assigned specifically to chlorophyll-d, how these bands shifted, and how their intensities changed, upon cation formation was never considered. Without this information it is difficult to draw unambiguous conclusions from the FTIR difference spectra. To gain a more detailed understanding of cation induced shifting of bands associated with vibrational modes of P740 we have used density functional theory to calculate the vibrational properties of a chlorophyll-d model in the neutral, cation and anion states. These calculations are shown to be of considerable use in interpreting bands in (P740(+)-P740) FTIR difference spectra. Our calculations predict that the 3(1) formyl C-H mode of chlorophyll-d upshifts/downshifts upon cation/anion formation, respectively. The mode intensity also decreases/increases upon cation/anion formation, respectively. The cation induced bandshift of the 3(1) formyl C-H mode of chlorophyll-d is also strongly dependant on the dielectric environment of the chlorophyll-d molecules. With this new knowledge we reassess the interpretation of bands that were assigned to 3(1) formyl C-H modes of chlorophyll-d in (P740(+)-P740) FTIR difference spectra. Considering our calculations in combination with (P740(+)-P740) FTIR DS we find that the most likely conclusions are that P740 is a dimeric Chl-d species, in an environment of low effective dielectric constant ( approximately 2-8). In the P740(+) state, charge is asymmetrically distributed over the two Chl-d pigments in a roughly 60:40 ratio.

Identification of the special pair of photosystem II in a chlorophyll d-dominated cyanobacterium

The composition of photosystem II (PSII) in the chlorophyll (Chl) d-dominated cyanobacterium Acaryochloris marina MBIC 11017 was investigated to enhance the general understanding of the energetics of the PSII reaction center. We first purified photochemically active complexes consisting of a 47-kDa Chl protein (CP47), CP43' (PcbC), D1, D2, cytochrome b(559), PsbI, and a small polypeptide. The pigment composition per two pheophytin (Phe) a molecules was 55 +/- 7 Chl d, 3.0 +/- 0.4 Chl a, 17 +/- 3 alpha-carotene, and 1.4 +/- 0.2 plastoquinone-9. The special pair was detected by a reversible absorption change at 713 nm (P713) together with a cation radical band at 842 nm. FTIR difference spectra of the specific bands of a 3-formyl group allowed assignment of the special pair. The combined results indicate that the special pair comprises a Chl d homodimer. The primary electron acceptor was shown by photoaccumulation to be Phe a, and its potential was shifted to a higher value than that in the Chl a/Phe a system. The overall energetics of PSII in the Chl d system are adjusted to changes in the redox potentials, with P713 as the special pair using a lower light energy at 713 nm. Taking into account the reported downward shift in the potential of the special pair of photosystem I (P740) in A. marina, our findings lend support to the idea that changes in photosynthetic pigments combine with a modification of the redox potentials of electron transfer components to give rise to an energetic adjustment of the total reaction system.