Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature.

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.

West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.

Characterization of semiconductor materials using synchrotron radiation-based near-field infrared microscopy and nano-FTIR spectroscopy.

We describe the application of scattering-type near-field optical microscopy to characterize various semiconducting materials using the electron storage ring Metrology Light Source (MLS) as a broadband synchrotron radiation source. For verifying high-resolution imaging and nano-FTIR spectroscopy we performed scans across nanoscale Si-based surface structures. The obtained results demonstrate that a spatial resolution below 40 nm can be achieved, despite the use of a radiation source with an extremely broad emission spectrum. This approach allows not only for the collection of optical information but also enables the acquisition of near-field spectral data in the mid-infrared range. The high sensitivity for spectroscopic material discrimination using synchrotron radiation is presented by recording near-field spectra from thin films composed of different materials used in semiconductor technology, such as SiO2, SiC, SixNy, and TiO2.

Infrared microspectroscopy detects protein misfolding cyclic amplification (PMCA)-induced conformational alterations in hamster scrapie progeny seeds.

The self-replicative conformation of misfolded prion proteins (PrP) is considered a major determinant for the seeding activity, infectiousness, and strain characteristics of prions in different host species. Prion-associated seeding activity, which converts cellular prion protein (PrP(C)) into Proteinase K-resistant, infectious PrP particles (PrP(TSE)), can be monitored in vitro by protein misfolding cyclic amplification (PMCA). Thus, PMCA has been established as a valuable analytical tool in prion research. Currently, however, it is under discussion whether prion strain characteristics are preserved during PMCA when parent seeds are amplified in PrP(C) substrate from the identical host species. Here, we report on the comparative structural analysis of parent and progeny (PMCA-derived) PrP seeds by an improved approach of sensitive infrared microspectroscopy. Infrared microspectroscopy revealed that PMCA of native hamster 263K scrapie seeds in hamster PrP(C) substrate caused conformational alterations in progeny seeds that were accompanied by an altered resistance to Proteinase K, higher sedimentation velocities in gradient ultracentrifugations, and a longer incubation time in animal bioassays. When these progeny seeds were propagated in hamsters, misfolded PrP from brain extracts of these animals showed mixed spectroscopic and biochemical properties from both parental and progeny seeds. Thus, strain modifications of 263K prions induced by PMCA seem to have been partially reversed when PMCA products were reinoculated into the original host species.

Observation of content and heterogeneity of poly-ß-hydroxybutyric acid (PHB) in Legionella bozemanii by vibrational spectroscopy.

Information on how cells respond to their environment, interact with each other, or undergo complex processes such as cellular differentiation or gene expression has been obtained mostly by interference from population-level data. Individual microorganisms, even those on supposedly "clonal" populations, may differ widely from each other in terms of their genetic composition, physiology, biochemistry, or behaviours. This genetic and phenotypic heterogeneity has important practical consequences for a number of relevant interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. Here we introduce vibrational spectroscopy to characterize Legionella bozemanii with respect to its content of poly-hydroxybutyric acid (PHB) and its distribution on both the population level and the single cell level.

Evaluation of tip-enhanced Raman spectroscopy for characterizing different virus strains.

Tip-enhanced Raman spectroscopy (TERS) is a highly sensitive spectroscopic technique which combines the advantages of optical spectroscopy with the requirements needed for the characterization of biological nano-structures. In this study, TERS was used to investigate the applicability of this spectroscopic technique for the detection of different virus strains like avipoxvirus and adeno-associated virus. TERS spectra obtained from different particles of the same virus strain show variations in relative peak intensities and positions of most spectral features observed. These spectral variations were higher for the larger avipoxvirus particles (∅≈350 nm) than for the smaller adeno-associated virus particles (∅≈26 nm).

Resonance Raman microscopy in combination with partial dark-field microscopy lights up a new path in malaria diagnostics.

Our goal is to produce a rapid and accurate diagnostic tool for malaria using resonance Raman spectroscopy to detect small inclusions of haemozoin in Plasmodium falciparum infected red blood cells. In pursuit of this aim we serendipitously discovered a partial dark-field effect generated by our experimental setup, which helps identify in thick blood films potential parasites that are normally difficult to see with conventional bright-field microscopy. The haemozoin deposits 'light up' and these can be selectively targeted with the Raman microscope to confirm the presence or absence of haemozoin by the strong 1569 cm(-1) band, which is a marker for haemozoin. With newly developed imaging Raman microscopes incorporating ultra-sensitive rapid readout CCDs it is possible to obtain spectra with a good signal-to-noise ratio in 1 second. Moreover, images from a smear of potentially infected cells can be recorded and analysed with multivariate methods. The reconstructed images show what appear to be sub-micron-inclusions of haemozoin in some cells indicating that the technique has potential to identify low pigmented forms of the parasite including early trophozoite-stage infected cells. Further work is required to unambiguously confirm the presence of such forms through systematic staining but the results are indeed promising and may lead to the development of a new Raman-based malaria diagnostic.

Phenotypic heterogeneity within microbial populations at the single-cell level investigated by confocal Raman microspectroscopy.

Single cells in genetically homogeneous microbial cultures exhibit marked phenotypic heterogeneity that is considered to bolster the fitness of the whole population. Heterogeneity on the single-cell level is typically masked in conventional studies of microbial populations, which rely on data averaged across thousands or millions of cells in a sample. Here we introduce confocal Raman microspectroscopy as a method for investigating and illustrating the spatial heterogeneity of microbial cell populations. By the use of three different test organisms as model systems, we show pronounced cellular heterogeneity even in colonies cultivated under laboratory conditions.

Correction of axial chromatic aberrations in confocal Raman microspectroscopic measurements of a single microbial spore.

Herein we describe a strategy for correcting the longitudinal or axial component of chromatic aberration in confocal Raman microspectroscopy. The method is based on measuring a vertical series of confocal Raman sections of samples by a high numerical aperture Raman microscope. Using the known characteristics of the wavelength-dependent focal shift of the optical system, the Raman intensities can be corrected to allow the rearrangement of Raman data from different focal planes. In the present study the computational correction routine was applied to an experimental data set of 4-dimensional (xyz spatial and the spectral dimension) confocal Raman spectra collected from single spores of Bacillus cereus. After correcting the axial component of the chromatic aberration, univariate and multivariate spectral parameters were obtained and used in the following for 3D segmentation and volume rendering on the basis of the structural and compositional information contained in the Raman spectra of the spore. Using univariate Raman intensities from defined functional group frequencies or k-means cluster membership values as a multivariate parameter for volume rendering, we demonstrate a high degree of correlation between confocal Raman microspectroscopy and the spores' morphology. In this paper we will also present cluster mean spectra which will be discussed in light of the presence of proteins and Ca-DPA, a calcium chelate of dipicolinic acid in the spore.

Adsorption of GST-PI3Kgamma at the air-buffer interface and at substrate and nonsubstrate phospholipid monolayers.

The recruitment of phosphoinositide 3-kinase gamma (PI3Kgamma) to the cell membrane is a crucial requirement for the initiation of inflammation cascades by second-messenger production. In addition to identifying other regulation pathways, it has been found that PI3Kgamma is able to bind phospholipids directly. In this study, the adsorption behavior of glutathione S-transferase (GST)-PI3Kgamma to nonsubstrate model phospholipids, as well as to commercially available substrate inositol phospholipids (phosphoinositides), was investigated by use of infrared reflection-absorption spectroscopy (IRRAS). The nonsubstrate phospholipid monolayers also yielded important information about structural requirements for protein adsorption. The enzyme did not interact with condensed zwitterionic or anionic monolayers; however, it could penetrate into uncompressed fluid monolayers. Compression to values above its equilibrium pressure led to a squeezing out and desorption of the protein. Protein affinity for the monolayer surface increased considerably when the lipid had an anionic headgroup and contained an arachidonoyl fatty acyl chain in sn-2 position. Similar results on a much higher level were observed with substrate phosphoinositides. No structural response of GST-PI3Kgamma to lipid interaction was detected by IRRAS. On the other hand, protein adsorption caused a condensing effect in phosphoinositide monolayers. In addition, the protein reduced the charge density at the interface probably by shifting the pK values of the phosphate groups attached to the inositol headgroups. Because of their strongly polar headgroups, an interaction of the inositides with the water molecules of the subphase can be expected. This interaction is disturbed by protein adsorption, causing the ionization state of the phosphates to change.

Do unsaturated phosphoinositides mix with ordered phosphadidylcholine model membranes?

Phosphoinositides have been shown to control membrane trafficking events by targeting proteins to specific cellular sites, which requires a tight regulation of phosphoinositide generation and turnover as well as a high degree of compartmentalization. To shed light on the processes that lead to the formation of phosphoinositide-enriched microdomains, mixed monolayers of phosphatidylcholine and dioleoyl-phosphatidylinositol (DOPtdIns) or dioleoyl-phosphatidylinositol-bisphosphate [DOPtdIns(4,5)P(2)] were investigated by isothermal area/pressure measurements, Brewster angle microscopy, and grazing incidence X-ray diffraction. The results are consistent with a charge-dependent formation of phosphatidylinositol-containing tightly packed phases. DOPtdIns is capable of mixing partially with condensed 1,2-distearoyl-phosphatidylcholine (DSPC) and of forming mixed crystals that differ significantly from those formed by pure DSPC. DOPtdIns(4,5)P(2) in mixtures with DSPC is, to a much larger extent, phase separated. The observed phase separation of the highly charged DOPtdIns(4,5)P(2) is presumably water stabilized by electrostatic interactions and hydrogen bonding. In biological systems, an enzymatic phosphorylation of phosphatidylinositol in mixed domains may cause their insolubility in ordered phosphatidylcholine areas and lead to a cooperative reorganization of the host lipid membrane. This strong cooperative effect underlines the important role of PtdIns(4,5)P(2) in signal transduction processes and suggests that the ability of phosphoinositides to induce or reduce long-range interactions in phospholipid mixtures is crucial.

Elemental analysis within the electrical double layer using total reflection X-ray fluorescence technique.

A simplified total reflection X-ray fluorescence (TRXF) technique is proposed for the study of the electrical double layer (EDL) near charged monolayers at the air-water interface. In contrast to the parent NTEF (near total external reflection X-ray fluorescence) method, TRXF uses a fixed angle of incidence (below the critical one) and abandons both "spatial resolution" (which is poor anyway) and "absolute calibration" with the bulk reference. These modifications reduce both the duration of experiments and the complexity of the data treatment by 1-2 orders of magnitude and turn TRXF into a truly simple tool for elemental analysis within the EDL. A few TRXF experiments appear sufficient to disprove the model of simultaneous binding of alkali earth metal cations and inorganic anions to negatively charged phospholipid monolayers as proposed in literature. Direct experimental support was provided to the essential feature of the EDL near highly charged interfaces: The main amount of counterions is concentrated in the thin inner part of the EDL irrespective of the electrolyte concentration in the bulk. A study of the counterion competition for the participation in the EDL of highly negatively charged behenylsulfate (BS) monolayers (resulting from packing density limitations) revealed that univalent Cs+ is quite competitive with divalent Ca2+ and Ba2+ (which contradicts the classical Gouy-Chapman model). If the univalent/divalent ion ratio in bulk is 9:1, the corresponding ratio in the EDL is ca. 1.5 for Cs+/Ca2+ and 0.5 for Cs+/Ba2+, whereas the model predicts 0.14 only. Bearing in mind packing density limitations, these values are consistent with a series of sizes for hydrated ions: Cs+ < Ba2+ < Ca2+.