Physical methods of analysis

The choice of analytical techniques for the solution of real analytical problems is governed not only by the characteristics of the individual methods, but also by the alternatives available. The capabilities of some methods of elemental analysis are considered and compared with those of selected techniques based upon sample irradiation with charged particles.     

Scaffold assembly based on genome rearrangement analysis

Advances in DNA sequencing technology over the past decade have increased the volume of raw sequenced genomic data available for further assembly and analysis. While there exist many algorithms for assembly of sequenced genomic material, they often experience difficulties in constructing complete genomic sequences. Instead, they produce long genomic subsequences (scaffolds), which then become a subject to scaffold assembly aimed at reconstruction of their order along genome chromosomes. The balance between reliability and cost for scaffold assembly is not there just yet, which inspires one to seek for new approaches to address this problem. We present a new method for scaffold assembly based on the analysis of gene orders and genome rearrangements in multiple related genomes (some or even all of which may be fragmented). Evaluation of the proposed method on artificially fragmented mammalian genomes demonstrates its high reliability. We also apply our method for incomplete anophelinae genomes, which expose high fragmentation, and further validate the assembly results with referenced-based scaffolding. While the two methods demonstrate consistent results, the proposed method is able to identify more assembly points than the reference-based scaffolding.     

Physical foundation of quantitative Auger analysis

The possibility of using an Auger peak height in the dN (E) /dE spectrum and an integrated N (E) spectrum as a measure of the Auger current is discussed and necessary relations are presented. The methods of the background determination are reviewed and discussed.

The relation between the Auger current and the atomic cancentration of a corresponding sample component is derived and the state of art in the field of theoretical and experimental determination of factors appearing in this relation (ionization cross-section, Auger transition probability. backscattering factor, and inelastic mean free path of Auger electrons) is presented.

Approaches to the quantitative Auger analysis (QAA) of homogeneous, isotropic samples, including corrections for matrix factors, are presented and discussed. Problems arising when heterogeneous samples are analyzed are discussed and practical approaches to such an analysis are presented.

The role of crystalline effects (the dependence of the Auger signal from crystalline samples on the direction of the primary electron beam and angular distribution of Auger electron emission from such samples) in QAA is discussed and examples of such crystalline effects are presented together with their physical foundation.

Some rules are suggested allowing the quantitative Auger analysis to be performed with the smallest possible error.     

Physical analysis of atom-symmetric top collisions

Presented is a study of the general features of rotationally inelastic atom-symmetric top collision systems. This was made possible by employing a newly-developed exponential distorted wave procedure to calculate cross sections rapidly and accurately. It is demonstrated that consideration of the symmetry properties of symmetric tops leads to a reduction in the dimensionality of scattering equations and significant labor savings. Physical trends observed in cross sections and rate constants are shown to be understandable in terms of energetic and coupling concepts.     

Development of capillary array DNA sequencers for genome analysis

Massive analysis of biological molecules is being successfully applied to elucidate various biological phenomena using techniques of molecular science. This new era was initiated by the Human Genome Project, which was supported by the development of various automated tools including DNA sequencers and DNA chips. A small project led by Akiyoshi Wada in Japan triggered the development of automated DNA analysis instruments. As one of the members of the project, the author has been engaged in developing DNA analyzers including capillary array DNA sequencers. Here, the principles and development of the main technologies related to capillary array DNA sequencers, which contributed to the completion of the Human Genome Project, are reviewed. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 000–000; 2010: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.200900010     

High performance liquid chromatographic strategy for the analysis of exopolysaccharides extracted from pathogenic bacteria.

A high performance liquid chromatographic (HPLC) method has been developed to permit the rapid comparison of acidic polysaccharides of diverse compositions and the sensitive determination of their constituents. It is based on two combined analyses of the polysaccharide hydrolysates--a separation of the released compounds by ion-moderated partition chromatography with UV detection at two wavelengths and a separation of the sugar dansylhydrazine derivatives by reversed phase chromatography. The former permits identification and quantitation of uronic and carboxylic acids, the latter permits more sensitive and specific determination of the neutral aldoses. Some bacterial exopolysaccharides have been used to demonstrate the validity of this HPLC procedure for the chemical characterization of uronic acid-containing polysaccharides. This method appears to be useful for studying capsular polysaccharides, which are involved in the evasion of phagocytosis by pathogenic bacteria.     

Genome level analysis of bacteriocins of lactic acid bacteria

Bacteriocins are antimicrobial peptides which are ribosomally synthesized by mainly all bacterial species. LABs (lactic acid bacteria) are a diverse group of bacteria that include around 20 genera of various species. Though LABs have a tremendous potential for production of anti-microbial peptides, this group of bacteria is still underexplored for bacteriocins. To study the diversity among bacteriocin encoding clusters and the putative bacteriocin precursors, genome mining was performed on 20 different species of LAB not reported to be bacteriocin producers. The phylogenetic tree of gyrB, rpoB, and 16S rRNA were constructed using MEGA6 software to analyze the diversity among strains. Putative bacteriocins operons identified were found to be diverse and were further characterized on the basis of physiochemical properties and the secondary structure. The presence of at least two cysteine residues in most of the observed putative bacteriocins leads to disulphide bond formation and provide stability. Our data suggests that LABs are prolific source of low molecular weight non modified peptides.     

Hundredfold productivity of genome analysis by introduction of microtemperature-gradient gel electrophoresis

Genome profiling, which employs temperature-gradient gel electrophoresis (TGGE) for DNA analysis, has recently been developed in identifying species by genotype. However, the performance of this technology like the general applications of TGGE was, though highly informative, limited in its ability due to methodological reasons. This study demonstrates that minimization of the gel for TGGE, to around one-tenth of its conventional size (approximately 2 cm), can be successfully introduced, resulting in a hundredfold higher performance (total evaluation of time, cost, and degree of parallel operations) than that of the conventional. Reproducibility was evaluated from the measures of the pattern similarity scores (PaSS) between band patterns (genome profiles) obtained with the conventional TGGE, and that with micro-TGGE (microTGGE) developed here, after extracting a set of featuring points from genome profiles. Size minimization, which leads to the reduction of the amount of samples required (cost-saving), is another great advantage, enhancing the employment of multicolor fluorescence technology. Since the further development of microbe-related fields such as epidemiology and microbial ecology inevitably require knowledge based on the identification of a great number of species and strains, microbe-related fields will receive the most optimal benefits from the technological improvements attained here.     

Physical procedures for the analysis of mixtures of polychloroethanes

A mixture of seven polychloroethanes has been analysed by fractionation into binary mixtures using a combination of continuous fractionation and the technique of total reflux with intermittent take-off. The binary mixtures were analysed by refractive index measurements. The relationship between binary mixture refractive index and component mass fraction was found to be linear. The temperature dependence of the refractive indices of the polychloroethanes over the range, 15–35°, was also determined.     

Physical adsorption analysis of intact supported MFI zeolite membranes

We compare the adsorption properties of intact supported silicalite membranes with those of silicalite powder and of alumina supports using nitrogen and argon as adsorbates at 77 K. We disentangle contributions from the membrane and support and find that the support contributes significantly to the total quantity adsorbed due to its relative thickness. The micropore-filling regions of the adsorption isotherms of the powder and the supported membrane are nearly identical for the membranes studied, but the isotherms differ at higher pressures--the supported membranes exhibit a much higher quantity adsorbed than the powders. Despite this difference, no hysteresis is observed in the membrane isotherms, indicating a lack of mesoporosity (pores in the 2-50 nm range) in either membrane or support for this preparation. We estimate argon transport fluxes at steady state by assuming surface diffusion with both a constant and concentration-dependent Maxwell-Stefan diffusion coefficient in the zeolite and the support. Further, we use the respective adsorption isotherms to determine the thermodynamic correction factors--that is, the ratios of the Fick and Maxwell-Stefan diffusion coefficients--required to solve the diffusion equation. The estimated argon flux is virtually the same using adsorption data from powders and membranes. For the relatively thick supports used in our study (approximately 2 mm), we find that the support exerts a much greater influence on the predicted fluxes for a wide range of values of the ratio of the support to zeolite diffusion coefficients. We emphasize that the results are specific to the architecture of the supported membranes studied, and thus, the results should be interpreted accordingly.     

Classification for dimethylarsenate-decomposing bacteria using a restrict fragment length polymorphism analysis of 16S rRNA genes.

A new monitoring system for bacterial communities involving dimethylarsinic acid (DMAA) decomposition was provided by combining the MPN (Most Probable Number) method and RFLP (restriction-fragment-length polymorphism analysis). The abundance of DMAA decomposing bacteria was estimated by the MPN method using a bacterial culture medium, which included DMAA as the sole carbon source, indicating bacterial cell densities of 1700 cells/ml in Lake Kahokugata and 330 cells/ml in Lake Kibagata. After isolating the dominant bacteria using agar plates, the isolates were classified into some genotype groups by RFLP analysis using 16S rDNA sequences. Classification of the RFLP analysis indicated that 14 isolates of Lake Kahokugata were classified into 6 types, which included 2 dominant types related to genus Pseudomonas, while 8 isolates of Lake Kibagata displayed 6 types including one or two isolates. Moreover, the RFLP types were unique for each lake, suggesting that DMAA decomposing bacteria were specific for the aquatic environment related to the arsenic cycle. The activities of DMAA decomposition mostly matched with the RFLP type category of the isolates. Accordingly, combining the MPN method with the RFLP analysis will play an important role in elucidating the distributions and dynamics of the DMAA-decomposing bacterial community.     

Identification of Enterobacteriaceae bacteria by direct matrix-assisted laser desorptiom/ionization mass spectrometric analysis of whole cells.

Several members of Enterobacteriaceas were analyzed by matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometry (TOFMS). Characteristic mass spectral peaks and patterns were observed in the mass range of 2 to 20 kDa. The mass peaks reported to be reproducibly observed by previous researchers, which were claimed to serve as species/strain-specific biomarkers, are consistently observed in our current study. Despite the high degree of similarity found in the MALDI mass spectra within the enteric bacteria, minor yet notable differences existed to allow their differentiation. Five spectral peaks at m/z 4364, 5380, 6384, 6856, and 9540, generated reproducibly for each genus studied here, are assigned as family-specific biomarkers for the Family Enterobacteriaceae. The mass peaks at m/z 7324, 7724, 9136, and 9253 are assigned as genus-specific biomarkers for Salmonella. Some unique biomarkers characterizing the species and strains of E. coli are also presented.     

Permeability of the outer membrane of bacteria.

The outer membrane of Gram-negative bacteria is an attractive system for the study of the structure-function relationships in biological membranes. This membrane has, inter alia, the task of regulating the inflow of nutrients and outflow of waste products. Investigations with the aid of mutants showed that there are at least two general pathways for the diffusion of small molecules across the outer membrane: one for hydrophobic and one for hydrophilic compounds. In the case of the “hydrophobic pathway” the hydrophobic compound dissolves in the interior of the membrane and then crosses the membrane in accordance with the partition coefficient. In wild-type forms of enteric bacteria this pathway cannot be used—presumably owing to the absence of regions with phospholipid bilayers. Small hydrophilic molecules, on the other hand, penetrate the membrane through water-filled pores.     

Perturbation of the chemotactic tumbling of bacteria.

The bacterial sensing system has been studied on three levels. First, a quantitative method has been devised for measuring the "action spectrum" of the bacterium in response to a sudden addition of attractant. Second, a technique has been developed for the rapid isolation of mutants defective in the transmission part of the sensing system. Third, a study of the effects of light on the transmission system reveals two components, one which generates, tumbling and another which inhibits it.     

Selective and specific detection of sulfate-reducing bacteria using potentiometric stripping analysis

A fast, sensitive and reliable potentiometric stripping analysis (PSA) is described for the selective detection of the marine pathogenic sulfate-reducing bacterium (SRB), Desulforibrio caledoiensis. The chemical and electrochemical parameters that exert influence on the deposition and stripping of lead ion, such as deposition potential, deposition time and pH value were carefully studied. The concentration of SRB was determined in acetate buffer solution (pH 5.2) under the optimized condition (deposition potential of −1.3 V, deposition time of 250 s, ionic strength of 0.2 mol L⁻¹ and oxidant mercury (II) concentration of 40 mg L⁻¹). A linear relationship between the stripping response and the logarithm of the bacterial concentration was observed in the range of 2.3 × 10 to 2.3 × 10⁷ cfu mL⁻¹. In addition, the potentiometric stripping technique gave a distinct response to the SRB, but had no obvious response to Escherichia coli. The measurement system has a potential for further applications and provides a facile and sample method for detection of pathogenic bacteria.     

Micro-impedance cytometry for detection and analysis of micron-sized particles and bacteria

The sensitivity of a microfluidic impedance flow cytometer is governed by the dimensions of the sample analysis volume. A small volume gives a high sensitivity, but this can lead to practical problems including fabrication and clogging of the device. We describe a microfluidic impedance cytometer which uses an insulating fluid to hydrodynamically focus a sample stream of particles suspended in electrolyte, through a large sensing volume. The detection region consists of two pairs of electrodes fabricated within a channel 200 μm wide and 30 μm high. The focussing technique increases the sensitivity of the system without reducing the dimensions of the microfluidic channel. We demonstrate detection and discrimination of 1 μm and 2 μm diameter polystyrene beads and also Escherichia coli. Impedance data from single particles are correlated with fluorescence emission measured simultaneously. Data are also compared with conventional flow cytometry and dynamic light scattering: the coefficient of variation (CV) of size is found to be comparable between the systems.     

Physical analysis of the diatomic “chemical” energy components

 The recent “chemical energy component analysis” permits the total energy of a molecule to be presented approximately but to good accuracy as a sum of atomic and diatomic energy contributions. Here the diatomic energy components are further decomposed into terms of different physical origin: electrostatics (in point-charge approximation and the distributed charge corrections), exchange effects, diatomic overlap and atomic basis extension terms. This analysis may provide us with a deeper insight into the factors influencing both the chemical bonds and the nonbonded interatomic interactions. Received: 6 May 2002 / Accepted: 13 November 2002 / Published online: 19 March 2003 Acknowledgements. The authors are indebted to the Hungarian Scientific Research Fund for partial financial support (grant no. OTKA T29716). Correspondence to: I. Mayer e-mail: mayer@chemres.hu     

pH-inducible beta-glucosidase and beta-glucuronidase of intestinal bacteria.

beta-Glucosidase and beta-glucuronidase of human and rat fecal bacteria were induced by cultivation in alkaline media although their growths were not affected. When a bacterium isolated from human feces producing each enzyme was cultured in a medium at pH 5 for 12-15 h and then adjusted to pH 8, beta-glucosidase and beta-glucuronidase were induced 9.2-fold and 11.5-fold, respectively.