Alexandre I. Tsapin

Hollow cathode ion lasers for deep ultraviolet Raman spectroscopy and fluorescence imaging

This article describes the development of hollow cathode ion lasers and their use in constructing an ultraviolet micro-Raman spectrograph with native fluorescence imaging capability. Excitation at 224.3 nm is provided by a helium–silver hollow cathode metal ion laser and at 248.6 nm by a neon–copper hollow cathode metal ion laser. Refractive microscope objectives focus chopped continuous wave laser light on a sample and collect 180° scattered photons. Imaging is accomplished by broadband visible illumination and by deep ultraviolet laser induced excitation of visible wavelength native fluorescence in untagged micro‐organisms. This makes possible a detection strategy employing rapid imaging with laser excitation to locate regions of native fluorescence activity, followed by deep ultraviolet resonance Raman spectroscopy of the identified fluorescent sites. We have employed this probe for in situ detection of micro‐organisms on mineral and soil substrates. We present here the deep ultraviolet resonance Raman...

Thioalkalimicrobium cyclicum sp. nov. and Thioalkalivibrio jannaschii sp. nov., novel species of haloalkaliphilic, obligately chemolithoautotrophic sulfur-oxidizing bacteria from hypersaline alkaline Mono Lake (California)

Two strains of haloalkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria were isolated from the oxygen-sulfide interface water layer of stratified alkaline and saline Mono Lake, California, USA. Strain ALM 1T was a dominant species in enrichment on moderate-saline, carbonate-buffered medium (0.6 M total Na+, pH 10) with thiosulfate as an energy source and nitrate as a nitrogen source. Cells of ALM 1T are open ring-shaped and are non-motile. It has a high growth rate and activity of thiosulfate and sulfide oxidation and very low sulfur-oxidizing activity. Genetic comparison and phylogenetic analysis suggested that ALM 1T (= DSM 14477T = JCM 11371T) represents a new species of the genus Thioalkalimicrobium in the gamma-Proteobacteria, for which the name Thioalkalimicrobium cyclicum sp. nov. is proposed. Another Mono Lake isolate, strain ALM 2T, dominated in enrichment on a medium containing 2 M total Na+ (pH 10). It is a motile vibrio which tolerates up to 4 M Na+ and produces a membrane-bound yellow pigment. Phylogenetic analysis placed ALM 2T as a member of genus Thioalkalivibrio in the gamma-Proteobacteria, although its DNA hybridization with the representative strains of this genus was only about 30%. On the basis of genetic and phenotypic properties, strain ALM 2T (= DSM 14478T = JCM 11372T) is proposed as Thioalkalivibrio jannaschii sp. nov..

Identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in Shewanella oneidensis strain MR1

ABSTRACT Two abundant, low-redox-potential cytochromesc were purified from the facultative anaerobeShewanella oneidensis strain MR1 grown anaerobically with fumarate. The small cytochrome was completely sequenced, and the genes coding for both proteins were cloned and sequenced. The small cytochrome c contains 91 residues and four heme binding sites. It is most similar to the cytochromes c fromShewanella frigidimarina (formerly Shewanella putrefaciens) NCIMB400 and the unclassified bacterial strain H1R (64 and 55% identity, respectively). The amount of the small tetraheme cytochrome is regulated by anaerobiosis, but not by fumarate. The larger of the two low-potential cytochromes contains tetraheme and flavin domains and is regulated by anaerobiosis and by fumarate and thus most nearly corresponds to the flavocytochromec-fumarate reductase previously characterized fromS. frigidimarina to which it is 59% identical. However, the genetic context of the cytochrome genes is not the same for the twoShewanella species, and they are not located in multicistronic operons. The small cytochrome c and the cytochrome domain of the flavocytochrome c are also homologous, showing 34% identity. Structural comparison shows that theShewanella tetraheme cytochromes are not related to theDesulfovibrio cytochromes c3but define a new folding motif for small multiheme cytochromesc.

Classification of Organic and Biological Materials with Deep Ultraviolet Excitation

We show that native fluorescence can be used to differentiate classes or groups of organic molecules and biological materials when excitation occurs at specific excitation wavelengths in the deep ultraviolet (UV) region. Native fluorescence excitation–emission maps (EEMs) of pure organic materials, microbiological samples, and environmental background materials were compared using excitation wavelengths between 200–400 nm with emission wavelengths from 270 to 500 nm. These samples included polycyclic aromatic hydrocarbons (PAHs), nitrogen- and sulfur-bearing organic heterocycles, bacterial spores, and bacterial vegetative whole cells (both Gram positive and Gram negative). Each sample was categorized into ten distinct groups based on fluorescence properties. Emission spectra at each of 40 excitation wavelengths were analyzed using principal component analysis (PCA). Optimum excitation wavelengths for differentiating groups were determined using two metrics. We show that deep UV excitation at 235 (±2) nm optimally separates all organic and biological groups within our dataset with >90% confidence. For the specific case of separation of bacterial spores from all other samples in the database, excitation at wavelengths less than 250 nm provides maximum separation with >6σ confidence.

Expression of a tetraheme protein, Desulfovibrio vulgaris Miyazaki F cytochrome c(3), in Shewanella oneidensis MR-1.

ABSTRACT Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F was successfully expressed in the facultative aerobe Shewanella oneidensis MR-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. A derivative of the broad-host-range plasmid pRK415 containing the cytochrome c3 gene fromD. vulgaris Miyazaki F was used for transformation ofS. oneidensis MR-1, resulting in the production of protein product that was indistinguishable from that produced by D. vulgaris Miyazaki F, except for the presence of one extra alanine residue at the N terminus.

Fourier transform infrared spectroscopy for Mars science

Presented here is a Fourier transform infrared spectrometer (FTIR) for field studies that serves as a prototype for future Mars science applications. Infrared spectroscopy provides chemical information that is relevant to a number of Mars science questions. This includes mineralogical analysis, nitrogen compound recognition, truth testing of remote sensing measurements, and the ability to detect organic compounds. The challenges and scientific opportunities are given for the in situ FTIR analysis of Mars soil and rock samples. Various FTIR sampling techniques are assessed and compared to other analytical instrumentation. The prototype instrument presented is capable of providing field analysis in a Mars analog Antarctic environment. FTIR analysis of endolithic microbial communities in Antarctic rocks and a Mars meteor are given as analytical examples.

Bimodal loop-gap resonator

Abstract A bimodal loop-gap resonator for electron-electron double resonance at X band is described. Considerable detail is given on frequency tuning; in one of the geometries described, a total tuning range of 500 MHz in the difference of the resonant frequencies of the two modes was achieved. The hypothesis is made that bimodal loop-gap resonators, because of their relatively low Q values, offer opportunities to arrive at structures that are more practical than bimodal cavities for routine EPR use. Data appear to support this hypothesis.

Water and surface contamination monitoring using deep UV laser induced native fluorescence and Raman spectroscopy

Reagentless water and surface sensors employing laser induced native fluorescence (LINF) and resonance Raman spectroscopy (RRS) in the deep UV are making significant progress in detecting chemical and biological targets and differentiating them against a wide range of background materials. Methods for optimizing sensor performance for specific target and backgrounds materials will be discussed in relationship to closed industrial environments and open natural environments. Limits of detection and chemical specificity will be discussed for high and low spectral resolution systems for a wide range of compounds and composite particles such as spores and cells. Detection and identification of single spores at working distance of several meters is illustrated. A range of sensors will be described along with their physical and performance specifications including sample, sipper and immersion sensors for water and fixed point and scanner systems for surfaces. In addition, the use of UV LINF and RRS for detection in capillary electrophoresis and liquid chromatography will be described with limits of detection in the range of a few nmol L-1.

XAS investigations of Fe(VI).

Recent attention has been given to a reexamination of results from the early Viking missions to Mars that suggested the presence of one or more strong oxidants in Martian soil. Since Fe is one of the main constituents of the Martian surface and Fe(VI) is known to be a highly reactive, strong oxidant, we have made XANES and EXAFS measurements of Fe(II), Fe(III), Fe(IV), and Fe(VI) in solid and solution forms. Results from these studies indicate a preedge XANES feature from Fe(VI) samples similar to that commonly seen from Cr(VI) samples. Results of first shell analysis indicate a linear relationship between the Fe-O bondlength and Fe valence state.

Marinospirillum celere sp. nov., a novel haloalkaliphilic, helical bacterium isolated from Mono Lake.

Two strains of a Gram-negative, helical, haloalkaliphilic bacterium were isolated from Mono Lake (USA). Both strains were mesophilic and grew between 13 and 55 degrees C, with optimum growth at 35-45 degrees C. The optimum pH for growth was 9.5. Growth was observed at NaCl concentrations of 0.5-12% (w/v), with optimum growth at 2% NaCl. Both isolates were motile by means of bipolar tuft flagella, coccoid body-forming and strictly aerobic. It was concluded that they belong to the same species, based on DNA-DNA hybridization values (95% DNA relatedness). DNA G+C contents of the novel strains were 52.1 and 52.3 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were shown to be related closely to the members of the genus Marinospirillum (family Oceanospirillaceae, class Gammaproteobacteria). Sequence similarity of strain v1c_Sn-redT to the type strains of Marinospirillum alkaliphilum, Marinospirillum minutulum, Marinospirillum megaterium and Marinospirillum insulare was 95.0, 92.7, 91.8 and 91.8%, respectively. Chemotaxonomic data [major ubiquinone, Q8; major fatty acids, C18:1(n-7) and C16:0] and physiological and biochemical tests supported the affiliation of the novel strains to the genus Marinospirillum as members of a novel species, for which the name Marinospirillum celere sp. nov. is proposed, with the type strain v1c_Sn-redT (=LMG 24610T=VKM 2416T).