Evaluation of aromatic amino acids as potential biomarkers in breast cancer by Raman spectroscopy analysis

The scope of the work undertaken in this paper was to explore the feasibility and reliability of using the Raman signature of aromatic amino acids as a marker in the detection of the presence of breast cancer and perhaps, even the prediction of cancer development in very early stages of cancer onset. To be able to assess this hypothesis, we collected most recent and relevant literature in which Raman spectroscopy was used as an analytical tool in the evaluation of breast cell lines and breast tissue, re-analyzed all the Raman spectra, and extracted all spectral bands from each spectrum that were indicative of aromatic amino acids. The criteria for the consideration of the various papers for this study, and hence, the inclusion of the data that they contained were two-fold: (1) The papers had to focus on the characterization of breast tissue with Raman spectroscopy, and (2) the spectra provided within these papers included the spectral range of 500-1200 cm-1, which constitutes the characteristic region for aromatic amino acid vibrational modes. After all the papers that satisfied these criteria were collected, the relevant spectra from each paper were extracted, processed, normalized. All data were then plotted without bias in order to decide whether there is a pattern that can shed light on a possible diagnostic classification. Remarkably, we have been able to demonstrate that cancerous breast tissues and cells decidedly exhibit overexpression of aromatic amino acids and that the difference between the extent of their presence in cancerous cells and healthy cells is overwhelming. On the basis of this analysis, we conclude that it is possible to use the signature Raman bands of aromatic amino acids as a biomarker for the detection, evaluation and diagnosis of breast cancer.

Branched-chain and aromatic amino acids and cardiometabolic risk in Black African and Asian Indian populations

INTRODUCTION

Studies have shown that systemic levels of branched-chain amino acids (BCAAs) and aromatic amino acids (AAAs) are elevated in cardiometabolic diseases (CMDs) in populations resident in high income countries. However, little is known about the association of BCAAs and AAAs with metabolic syndrome and its components in Asian Indian (AI) and Black African (BA) populations.

OBJECTIVE

The aim of this study was to describe the association of BCAAs and AAAs with the metabolic syndrome, its individual components and insulin resistance in AI and BA populations.

METHODS

Serum samples collected from AI (n = 349) and BA (n = 369) subjects were used to measure levels of BCAAs and AAAs by ultra-pressure liquid chromatography tandem mass spectrometry (UPLC-MS/MS). Anthropometric, demographic and cardiometabolic variables were measured in all subjects.

RESULTS

The sum of BCAAs and AAAs was higher in AIs compared to BAs. The BCAAs and AAAs were positively associated with insulin resistance, metabolic syndrome and its individual components. This was particularly the case for AI subjects, in unadjusted regression models. However, these associations were non-significant after adjusting for co-variates, particularly visceral adipose tissue (VAT). Triglyceride levels were significantly associated with valine and leucine levels in BAs even after adjustment for co-variates. Lastly, we found that fasting circulatory BCAA and AAA levels are strongly correlated with VAT in both populations.

CONCLUSION

This study identified specific associations of serum valine and leucine levels with triglycerides in BAs. The association of amino acids with CMDs was observed in AIs, but was found to be the result of confounding by VAT. Further studies are required to determine whether BCAAs and AAAs are aetiological factors in CMDs and how VAT modulates their serum levels.

Targeted Metabolomic Analysis of a Mucopolysaccharidosis IIIB Mouse Model Reveals an Imbalance of Branched-Chain Amino Acid and Fatty Acid Metabolism

Mucopolysaccharidoses (MPSs) are inherited disorders of the glycosaminoglycan (GAG) metabolism. The defective digestion of GAGs within the intralysosomal compartment of affected patients leads to a broad spectrum of clinical manifestations ranging from cardiovascular disease to neurological impairment. The molecular mechanisms underlying the progression of the disease downstream of the genetic mutation of genes encoding for lysosomal enzymes still remain unclear. Here, we applied a targeted metabolomic approach to a mouse model of PS IIIB, using a platform dedicated to the diagnosis of inherited metabolic disorders, in order to identify amino acid and fatty acid metabolic pathway alterations or the manifestations of other metabolic phenotypes. Our analysis highlighted an increase in the levels of branched-chain amino acids (BCAAs: Val, Ile, and Leu), aromatic amino acids (Tyr and Phe), free carnitine, and acylcarnitines in the liver and heart tissues of MPS IIIB mice as compared to the wild type (WT). Moreover, Ala, Met, Glu, Gly, Arg, Orn, and Cit amino acids were also found upregulated in the liver of MPS IIIB mice. These findings show a specific impairment of the BCAA and fatty acid catabolism in the heart of MPS IIIB mice. In the liver of affected mice, the glucose-alanine cycle and urea cycle resulted in being altered alongside a deregulation of the BCAA metabolism. Thus, our data demonstrate that an accumulation of BCAAs occurs secondary to lysosomal GAG storage, in both the liver and the heart of MPS IIIB mice. Since BCAAs regulate the biogenesis of lysosomes and autophagy mechanisms through mTOR signaling, impacting on lipid metabolism, this condition might contribute to the progression of the MPS IIIB disease.

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

Electroactive type IV pili, or e-pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e-pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22-aa aromatic gaps and aromatic amino acids at residues 1, 24, 27, 50 and/or 51, and 32 and/or 57) to search for putative e-pilin genes in metagenomes from diverse ecosystems with active microbial metal cycling. Environmental putative e-pilins were diverse in length and phylogeny, and included truncated e-pilins in Geobacter spp., as well as longer putative e-pilins in Fe(II)-oxidizing Betaproteobacteria and Zetaproteobacteria.

Physiological performance of glyphosate and imazamox mixtures on Amaranthus palmeri sensitive and resistant to glyphosate

The herbicides glyphosate and imazamox inhibit the biosynthetic pathway of aromatic amino acids (AAA) and branched-chain amino acids (BCAA), respectively. Both herbicides share several physiological effects in the processes triggered in plants after herbicide application that kills the plant, and mixtures of both herbicides are being used. The aim of this study was to evaluate the physiological effects in the mixture of glyphosate and imazamox in glyphosate-sensitive (GS) and -resistant (GR) populations of the troublesome weed Amaranthus palmeri. The changes detected in the physiological parameters after herbicide mixtures application were similar and even less to the changes detected after individual treatments. This pattern was detected in shikimate, amino acid and carbohydrate content, and it was independent of the EPSPS copy number, as it was detected in both populations. In the case of the transcriptional pattern of the AAA pathway after glyphosate, interesting and contrary interactions with imazamox treatment were detected for both populations; enhancement of the effect in the GS population and alleviation in the GR population. At the transcriptional level, no cross regulation between AAA and BCAA inhibitors was confirmed. This study suggests that mixtures are equally or less toxic than herbicides alone, and would implicate careful considerations when applying the herbicide mixtures.

Tyrosine Induced Metabolome Alterations of Penicillium roqueforti and Quantitation of Secondary Key Metabolites in Blue-Mold Cheese

To map qualitative and quantitative metabolome alterations when Penicillium roqueforti is grown in an environment where l-tyrosine levels are perturbed, the recently established differential off-line LC-NMR (DOLC-NMR) approach was successfully applied in connection with an absolute metabolite quantitation using a quantitative ¹H NMR protocol following the ERETIC 2 (Electronic REference To access In vivo Concentrations) methodology. Among the 23 influenced metabolites, amino acid degradation products like 2-(4-hydroxyphenyl)acetic acid and 2-(3,4-dihydroxyphenyl)acetic acid underwent a tremendous upregulation in the amino acid perturbed approach. Moreover, the output of secondary metabolites like andrastin A, eremofortin B, and the tetrapeptide d-Phe-l-Val-d-Val-l-Tyr was affected in the case of the presence or absence of the added aromatic amino acid. Furthermore, the isolated secondary metabolites of P. roqueforti have been quantified for the first time in five divergent Penicillium isolates by means of a validated LC-ECHO-MS/MS method. This technique is used to compensate the effect of co-extracted matrix compounds during the analysis and to utilize quasi-internal standards to quantify all metabolites of interest accurately. This screening outlined the great variety between the different fungi of the same species. The metabolite spectra of wild-type fungi included more toxic intermediates compared to a selected fungi used as a starter culture for blue-mold cheese production. In addition, these secondary metabolites were quantified in commercially available white- and blue-mold cheese samples. The main differences between the analyte profiles of white and blue cheeses were linked to the impact of the used starter culture. Specific metabolites detected from P. roqueforti like andrastin A and B or roquefortine C could not be detected in white cheese. Among the blue cheese samples, different metabolite pattern could be observed regarding various P. roqueforti starter cultures.

Au Nanoparticles Deposited on Magnetic Carbon Nanofibers as the Ultrahigh Sensitive Substrate for Surface-Enhanced Raman Scattering: Detections of Rhodamine 6G and Aromatic Amino Acids

Surface-enhanced Raman scattering (SERS) is a unique spectroscopy that can offer high-sensitive detection for many molecules. Herein, the Au particles deposited on carbon nanofiber-encapsulated magnetic Ni nanoparticles (NPs) (Ni@CNFs@Au) have been successfully synthesized for SERS measurements. The Ni@CNFs@Au substrates have the advantages of a high SERS sensitivity and good magnetic response. The Ni@CNFs could be directly obtained from CO₂ hydrogenation on a Ni catalyst, which has been characterized as having rich carboxylic acid groups, graphitic structures, and a high surface area. The Ni@CNFs surface could effectively increase the density of hotspots during Au NP aggregation and influence the morphology of the Au nanostructures. The spherical shape, oval shape, and coral-like Au nanostructures were prepared on Ni@CNFs with various Au concentrations. Brunauer-Emmett-Teller, zeta potential, high-resolution transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy measurements were used to characterize the Ni@CNFs@Au samples. The Au NPs deposited on the Ni@CNFs presented a suitable oval shape, and an average size of ∼30-40 nm. The size allowed surprisingly ultrasensitive SERS detection of rhodamine 6G (R6G) with a resolution of approximately a single molecule under an excitation wavelength of 532 nm. Using 785 nm excitation, a low R6G concentration of ∼1 × 10^-14 M was detected. Moreover, the Ni@CNFs@Au substrates could be rapidly magnetically separated after adsorption. Phenylalanine and tyrosine amino acids, which are associated with the liver disease, were examined using SERS with the Ni@CNFs@Au substrate. Ultralow concentrations of ∼1 × 10^-11 M for phenylalanine and ∼1 × 10^-13 M for tyrosine were clearly measured. The Ni@CNFs@Au substrates exhibited applicability as excellent SERS detection platforms that combine high-sensitivity and rapid magnetic separation for various adsorption molecules.

Detecting Nonvolatile Life- and Nonlife-Derived Organics in a Carbonaceous Chondrite Analogue with a New Multiplex Immunoassay and Its Relevance for Planetary Exploration

Potential martian molecular targets include those supplied by meteoritic carbonaceous chondrites such as amino acids and polycyclic aromatic hydrocarbons and true biomarkers stemming from any hypothetical martian biota (organic architectures that can be directly related to once living organisms). Heat extraction and pyrolysis-based methods currently used in planetary exploration are highly aggressive and very often modify the target molecules making their identification a cumbersome task. We have developed and validated a mild, nondestructive, multiplex inhibitory microarray immunoassay and demonstrated its implementation in the SOLID (Signs of Life Detector) instrument for simultaneous detection of several nonvolatile life- and nonlife-derived organic molecules relevant in planetary exploration and environmental monitoring. By utilizing a set of highly specific antibodies that recognize D- or L- aromatic amino acids (Phe, Tyr, Trp), benzo[a]pyrene (B[a]P), pentachlorophenol, and sulfone-containing aromatic compounds, respectively, the assay was validated in the SOLID instrument for the analysis of carbon-rich samples used as analogues of the organic material in carbonaceous chondrites or even Mars samples. Most of the antibodies enabled sensitivities at the 1-10 ppb level and some even at the ppt level. The multiplex immunoassay allowed the detection of B[a]P as well as aromatic sulfones in a water/methanol extract of an Early Cretaceous lignite sample (c.a., 140 Ma) representing type IV kerogen. No L- or D-aromatic amino acids were detected, reflecting the advanced diagenetic stage and the fossil nature of the sample. The results demonstrate the ability of the liquid extraction by ultrasonication and the versatility of the multiplex inhibitory immunoassays in the SOLID instrument to discriminate between organic matter derived from life and nonlife processes, an essential step toward life detection outside Earth.

Effect of frozen storage duration and cooking on physical and oxidative changes in M. Gastrocnemius pars interna and M. Iliofiburalis of Rhea americana

This study was conducted to evaluate the effect of frozen storage time (30, 60, 90 or 180 days) and cooking (100 °C, 30 min) on the physical characteristics and oxidative stability of M. Gastrocnemius pars interna (GN) and M. Iliofiburalis (IF) of rhea americana. Physical parameters measured included thawing and cooking loss, colour parameters (L*a*b*), while oxidation was assessed by determining the TBA-RS, carbonyl and aromatic amino acid content. Prolonged frozen storage of rhea meat decreased lightness (L*), yellowness (b*), and increased the discoloration parameter hue angle and redness a*. During storage, muscle IF was more prone to lipid and myoglobin oxidation than muscle GN. Cooking loss declined with the increase of storage time and was higher in GN than in IF muscle. With cooking, TBA-RS, carbonyl content, and aromatic amino acids (phenylalanine, tyrosine, and tryptophan) were highly affected, but the extent of oxidation ranged according to muscle and duration of frozen storage.

Solid state 19F NMR parameters of fluorine-labeled amino acids. Part II: aliphatic substituents

A representative set of amino acids with aliphatic 19F-labels has been characterized here, following up our previous compilation of NMR parameters for single 19F-substituents on aromatic side chains. Their isotropic chemical shifts, chemical shift tensor parameters, intra-molecular 19F dipole-dipole couplings and temperature-dependent T1 and T2 relaxation times were determined by solid state NMR on twelve polycrystalline amino acid samples, and the corresponding isotropic 19F chemical shifts and scalar couplings were obtained in solution. Of particular interest are amino acids carrying a trifluoromethyl-group, because not only the 19F chemical shift but also the intra-CF3 homonuclear dipolar coupling can be used for structural studies of 19F-labeled peptides and proteins. The CF3-groups are further compared with CH2F-, CD2F-, and CD3-groups, using both 19F and 2H NMR to describe their motional behavior and to examine the respective linebroadening effects of the protonated and deuterated neighbors. We have also characterized two unnatural amino acids in which a CF3-label is rigidly connected to the backbone by a phenyl or bicyclopentyl moiety, and which are particularly well suited for structure analysis of membrane-bound polypeptides. The 19F NMR parameters of the polycrystalline amino acids are compared with data from the correspondingly labeled side chains in synthetic peptides.

Solid state 19F NMR parameters of fluorine-labeled amino acids. Part I: aromatic substituents

Structural parameters of peptides and proteins in biomembranes can be directly measured by solid state NMR of selectively labeled amino acids. The 19F nucleus is a promising label to overcome the low sensitivity of 2H, 13C or 15N, and to serve as a background-free reporter group in biological compounds. To make the advantages of solid state 19F NMR fully available for structural studies of polypeptides, we have systematically measured the chemical shift anisotropies and relaxation properties of the most relevant aromatic and aliphatic 19F-labeled amino acids. In this first part of two consecutive contributions, six different 19F-substituents on representative aromatic side chains were characterized as polycrystalline powders by static and MAS experiments. The data are also compared with results on the same amino acids incorporated in synthetic peptides. The spectra show a wide variety of lineshapes, from which the principal values of the CSA tensors were extracted. In addition, temperature-dependent T(1) and T(2) relaxation times were determined by 19F NMR in the solid state, and isotropic chemical shifts and scalar couplings were obtained in solution.

Comparison of collision-induced dissociation and electron-induced dissociation of singly protonated aromatic amino acids, cystine and related simple peptides using a hybrid linear ion trap-FT-ICR mass spectrometer

The gas-phase fragmentation reactions of singly protonated aromatic amino acids, their simple peptides as well as simple models for intermolecular disulfide bonds have been examined using a commercially available hybrid linear ion trap-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Low-energy collision-induced dissociation (CID) reactions within the linear ion trap are compared with electron-induced dissociation (EID) reactions within the FT-ICR cell. Dramatic differences are observed between low-energy CID (which occurs via vibrational excitation) and EID. For example, the aromatic amino acids mainly fragment via competitive losses of NH(3) and (H(2)O+CO) under CID conditions, while side-chain benzyl cations are major fragment ions under EID conditions. EID also appears to be superior in cleaving the S-S and S-C bonds of models of peptides containing an intermolecular disulfide bond. Systematic studies involving fragmentation as a function of electron energy reveal that the fragmentation efficiency for EID occurs at high electron energy (more than 10 eV) compared with the low-electron energy (less than 0.2 eV) typically observed for electron capture dissociation fragmentation. Finally, owing to similarities between the types of fragment ions observed under EID conditions and those previously reported in ultraviolet photodissociation experiments and the electron-ionization mass spectra, we propose that EID results in fragmentation via electronic excitation and vibrational excitation. EID may find applications in analyzing singly charged molecular ions formed by matrix-assisted laser desorption ionization.

Electronic and vibrational circular dichroism of aromatic amino acids by density functional theory

Structures of model compounds mimicking aromatic amino acid residues in proteins are optimized by density functional theory (DFT), assuming that the main-chain conformation was a random coil. Excitation energies and dipole and rotational strengths for the optimized structures were calculated based on time-dependent DFT (TD-DFT). The electronic circular dichroism (ECD) bands of the models were significantly affected by side-chain conformations. Hydration models of the aromatic residues were also subjected to TD-DFT calculations, and the ECD bands of these models were found to be highly perturbed by the hydration of the main-chain amide groups. In addition to calculating the random-coil conformation, we also performed TD-DFT calculations of the aromatic residue models, assuming that the main-chain conformation was an alpha-helix or beta-strand. As expected, the overall feature of the ECD bands was also perturbed by the main-chain conformations. Moreover, vibrational circular dichroism (VCD) spectra of the hydration models in a random-coil structure were simulated by DFT, which showed that the VCD spectra are more sensitive to the side-chain conformations than the ECD spectra. The present results show that analyses combining ECD and VCD spectroscopy and using DFT calculations can elucidate the main- and side-chain conformations of aromatic residues in proteins.

Reagentless identification of human bifidobacteria by intrinsic fluorescence

A new identification method for bifidobacteria species from the human gastrointestinal tract was developed based on the measurement and statistical analysis of the intrinsic fluorescence of aromatic amino acids (AAA) and nucleic acids (NA), following their excitation at 250 nm. The model was constructed by recording the fluorescence spectra of 53 Bifidobacterium strains of 10 different species, including the corresponding type strains, and validated by analyzing the spectra data from nine further problem strains. Principal components analysis (PCA) and factorial discriminant analysis (FDA) of the results showed the technique to distinguish between the isolates at the species level; the Bifidobacterium pseudolongum subspecies (globosum and pseudolongum) could also be distinguished. The proposed method provides a powerful, inexpensive and convenient means of rapidly identifying intestinal bifidobacteria, which could be of help for large probiotic surveys.

Vibrational spectra and normal coordinate analysis of diazepam, phenytoin and phenobarbitone

Vibrational spectroscopy is an important tool for the structural investigation of the organic molecules. In the present investigation, a normal coordinate analysis has been carried out on some anti-epileptic drugs, viz. diazepam, phenytoin and phenobarbitone. Diazepam is a derivative of benzodiazepine, phenytoin is a derivative of hydanation and pheonobarbitone is a barbiturate. The infrared spectra of the compounds are recorded in the region 4000-400 cm(-1) and Raman spectra are recorded in the region 3500-50 cm(-1). From the structural point of view, diazepam, phenytoin and phenobarbitone have been assumed to C(s) point group. A systematic set of symmetry coordinates has been constructed for these compounds and Wilson's FG matrix method has been applied for the normal coordinate analysis using general quadratic valance force field. The potential energy distribution is also calculated to check the vibrational band assignments.

Amino acid residues in Rag1 crucial for DNA hairpin formation

The Rag proteins carry out V(D)J recombination through a process mechanistically similar to cut-and-paste transposition. Specifically, Rag complexes form DNA hairpins through direct transesterification, using a catalytic Asp-Asp-Glu (DDE) triad in Rag1. How is sufficient DNA distortion introduced to allow hairpin formation? We hypothesized that, like certain transposases, the Rag proteins might use aromatic amino acid residues to stabilize a flipped-out base. Through in vivo and in vitro experiments and structural predictions, we identified residues in Rag1 crucial for hairpin formation. One of these, a conserved tryptophan (Trp893), probably participates in base-stacking interactions near the cleavage site, as do Trp298, Trp265 and Trp319 in the Tn5, Tn10 and Hermes transposases, respectively. Other residues surrounding the catalytic glutamate (YKEFRK) may share functional similarities with the YREK motif in IS4 family transposases.

Concentration measurements by PULCON using X-filtered or 2D NMR spectra

Sample concentrations can be measured by nuclear magnetic resonance (NMR) spectroscopy without an internal reference compound using pulse length based concentration determination (PULCON) with 1D NMR spectra. PULCON delivers most accurate results if the spectrum of the sample of interest contains a resolved resonance; but can also be applied to spectral regions with overlapping resonances. If the exact number of lines contributing to the overlapping spectral region is not known, a corresponding error makes the result less precise. The uncertainty about the number of contributing resonances can be reduced with experiments that discriminate different classes of resonances by filtering techniques or by extending PULCON to two-dimensional NMR spectra. We demonstrate the application of PULCON with a 1D 15N-filtered experiment where aromatic resonances of a protein can be observed without interference from 15N-bound protons. Further, we extend PULCON to 2D NMR spectra that permits to determine the exact number of resonances. This extension can readily be applied with sample that contain different solutes.

Characterization and quantification of eight water-soluble constituents in tubers of Pinellia ternata and in tea granules from the Chinese multiherb remedy Xiaochaihu-tang

In traditional Chinese medicine, multiple herbs are usually used in combination to generate the joint actions of a multiherb remedy. The recent development of LC-hyphenated techniques enables efficient and rapid profiling of the chemical constituent in extracts from multiherb remedies. Xiaochaihu-tang is a seven-herb remedy that has attracted a great deal of attention for reported ability to treat liver dysfunction. Dried tubers of Pinellia ternata (banxia in Chinese) is one of the ingredients, but its chemical contribution to Xiaochaihu-tang remains poorly understood. In the study presented here, LC-UV-MS, LC-MS-MS, and LC-NMR were used in a complementary manner to determine the nature and content of eight water-soluble constituents of banxia and their presence in various tea granules from Xiaochaihu-tang. Among the eight chemicals identified in banxia, cytidine, adenosine, tryptophan, uridine, and adenine are reported for the first time, while tyrosine, guanosine, and phenylalanine were previously described. These chemicals are also present in all of the samples of Xiaochaihu-tang granules, and the amounts of the chemicals ingested due to a daily dose of the multiherb remedies range from 0.008 to 6.3mg.

NCA nucleophilic radiofluorination on substituted benzaldehydes for the preparation of [18F]fluorinated aromatic amino acids

Nucleophilic aromatic substitution is a challenging task in radiochemistry. Therefore, a thorough evaluation and optimisation of this step is needed to provide a satisfactory tool for the routine preparation of [(18)F]fluorinated aromatic amino acids. Two methods, already proposed elsewhere, were evaluated and improved. The yields for the radiofluorination were increased whereas activity loss during solid phase extraction was observed. Radiochemical yields for the two methods were 92.7+/-5.5% (method 1) and 92.1+/-12.3% (method 2) for conversion and 11.1+/-2.8% (method 1) and 34.8+/-0.6% (method 2) for purification, respectively. In total, we demonstrate an optimised method for the preparation of this important class of [(18)F]fluorinated synthons for PET.

Growth and survival of bacteria implicated in sudden infant death syndrome on cot mattress materials

AIMS

To compare growth and survival of selected bacteria implicated in sudden infant death syndrome (SIDS) on cot mattress polyurethane (PU) inner-foams and on different types of cot mattress cover materials.

METHODS AND RESULTS

Escherichia coli, Staphylococcus aureus or Streptococcus pyogenes were inoculated onto swatches of new-unused cot mattress PU inner-foam and onto three types of cot mattress covers (polyvinyl chloride, cotton and polyester). The influence of inoculation cell density, relative humidity (RH) and temperature of incubation on survival was assessed by recovery of cells in 0.85% NaCl, with viable cell enumeration by plate counting on selective and differential media. Utilization of carbon and nitrogen sources within cot mattress PU was assessed by following growth on aqueous leachate from PU, and by colorimetric determination of aromatic amines. Good survival capability (>206 d) was shown by all three test species on PU inner-foam and on polyester mattress cover at high RH (75%), but only by Staph. aureus on PU at low RH (25%). Aqueous soluble material from PU foam supports bacterial growth; removal of aromatic amines from aqueous leachate from PU accompanies growth of Staph. aureus.

CONCLUSIONS

Staphylococcus aureus has good survival capability on cot mattress PU foam, even at low RH. Soluble material within PU can serve as carbon and nitrogen sources for bacterial growth.

SIGNIFICANCE AND IMPACT OF THE STUDY

Prolonged survival of Staph. aureus on PU at low RH could explain, in the context of the common bacterial toxins hypothesis, an increased risk of SIDS associated with used infant mattresses.

Chromatography and Computational Chemical Analysis for Drug Discovery

Analytical chemists have increasingly turned their attention to drug discovery and drug analysis and to solve fundamental questions of biological significance in physiology and genetics. New technologies have been developed, and a variety of instruments have been redesigned for biomedical applications. The development of high-performance liquid chromatography (HPLC) opened a new era in biorelated fields and allowed faster separations of fragile macromolecules. Capillary column gas chromatography (GC)/mass spectrometry (MS) have been used to achieve more powerful separation and to perform structural analysis of molecules, and laboratory automation including robotics has become a powerful trend in both analysis and synthesis. Liquid chromatography (LC)/MS is more suitable for biomedical applications than GC/MS because almost all biomolecules are heat sensitive. Furthermore, a combination of various mass spectrometers has been used even for proteins directly. Improving the sensitivity of nuclear magnetic resonance spectrometry (NMR) has permitted a direct connection with LC. Purification of biomolecules on-line by LC has been performed since the development of chip-electrophoresis, On the other hand, computational chemical analysis is a promising technique given the advancing the hardware and software for use in chemical fields. In this review, a combination of chromatography and computational chemistry for use in drug discovery studies is described. Fast LC analysis using a column switching technique was introduced for aromatic amino acid metabolites and guanidino compounds. Recent developments in related technologies are also included from review papers.

Identification by fluorescence spectroscopy of lactic acid bacteria isolated from a small-scale facility producing traditional dry sausages

Three different fluorescence spectra were recorded following excitation at 250 nm (aromatic amino acids+nucleic acids, AAA+NA), 316 nm (NADH) and 380 nm (FAD) for 20 type strain collections of lactic acid bacteria (LAB). Evaluation of the data using principal component analysis and factorial discriminant analysis showed a good discrimination of considered LAB at the genus, species and genus-species level. AAA+NA fluorophores showed the highest percentage of good classification. From AAA+NA spectra recorded on LAB isolated from a small-scale facility producing traditional dry sausages, we succeeded to identify 28 of 29 wild strains. This method allowed us to discriminate between Lactobacillus sakei subsp. carnosus and Lactobacillus sakei subsp. sakei. Thus, intrinsic fluorescence is an economical and powerful tool for the identification of wild LAB isolated from meat and meat products.

Evidence for dynamic clustering of carboxy-terminal aromatic amino acids in TonB-dependent energy transduction

Escherichia coli uses the proton motive force of the cytoplasmic membrane and TonB protein to energize the active transport of iron-siderophores and vitamin B12 across the outer membrane. TonB shuttles between the cytoplasmic and outer membranes, presumably during the course of energy transduction. Previous results indicated that the carboxy-terminal 65 amino acids of TonB are essential for both its outer membrane association and activity. A highly conserved region (residues 199-216) within this domain, predicted to be an amphipathic alpha-helix, was the initial focus of this study. Scanning mutagenesis indicated that only the aromatic residues F202, W213 and Y215 were individually important for activity. When the crystal structure of a dimeric TonB carboxy-terminus subsequently became available, we observed that two additional aromatic residues outside that region, F180 and F230, were potentially engaged in end-on hydrophobic interactions with the three residues identified previously. Changing these five aromatic residues individually to alanine reduced TonB activity. Surprisingly, however, each substitution exhibited a unique phenotypic profile with respect to ability to support [55Fe]-ferrichrome transport, sensitivity to colicins B, D, Ia and M or sensitivity to bacteriophage phi80. The phenotypic results suggested that the carboxy-terminus of TonB was a flexible and dynamic domain that could interact specifically with different ligands or transporters, perhaps through the aromatic residues. The possibility of interactions among all the aromatic residues was tested using double-mutant cycle analysis. All possible combinations of alanine substitutions were constructed, with the result that TonB containing any double-alanine substitution was inactive in the phenotypic assays, while retaining the ability to associate with the outer membrane. This synergistic, rather than additive, effect of the double mutants suggested that, consistent with the flexibility suggested by analysis of the single substitutions, all the aromatic residues might be capable of interacting with one another. A means of reconciling these results with the crystal structure is presented.

Aromatic side-chain interactions in proteins: Near- and far-sequence Tyr-X pairs

In the present study, an extensive analysis of the aromatic Tyr-X interactions is performed on a data set of 593 PDB structures, X being Phe, His, Tyr, and Trp. The nonredundant Tyr-X pairs (2645) were retained and separated by both the residue distance in the sequence and the secondary structures they bridge. Similar to the Phe-X and His-X pairs, the far-sequence Tyr-X pairs (X partner > five apart in the sequence: 74%) show comparable secondary structures and conformers for either type of X partner, in contrast with the near-sequence Tyr-X pairs (26%). As the Phe-X pairs, the near-sequence Tyr-X pairs stabilize secondary structures, mainly the alpha- helices (positions 1, 3, and 4) and the beta-strands (position 2). Like the Phe-X and His-X pairs, most far-sequence Tyr-X pairs (34%) bridge beta-strands and only 11% bridge helices. As for the Phe-X and the His-X pairs, the X partners of the far-sequence Tyr-X pairs are frequently "above" the tyrosine ring with tilted and normal rings, whereas the X partner of the near-sequence Tyr-X pairs gradually moves from the "aside" to the "above" location, together with a progressive decrease of normal and increase of parallel rings, respectively. Unlike the His-X pairs, the interactions of the hetroatom in Tyr-X pairs are only favored with a sequence position +4 and over, owing to the spatial accessibility of the heteroatom.

Analysis of some aromatic amines by means of derivative spectrophotometry

Derivative spectrophotometry (DS) was applied for the determination of selected aromatic amines in two-compound mixtures. Following pairs were analysed: o- and m-toluidine, o- and p-toluidine, m- and p-toluidine; o- and m-phenylenediamine (PDA), o- and p-PDA, m- and p-PDA; p,p'-diaminodiphenylmethane (DADPMe) and p-toluidine. The developed method of DS was used as a complementary technique to HPLC with DAD detector as it allows the determination of compounds, which give a common peak in a chromatographic system.

Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives

Tachyplesin I is a 17-residue peptide isolated from the horseshoe crab, Tachypleus tridentatus. It has high antimicrobial activity and adopts a beta-hairpin conformation in solution stabilized by two cross-strand disulfide bonds. We report an NMR structural investigation of wild-type tachyplesin I and three linear derivatives (denoted TPY4, TPF4, and TPA4 in which the bridging cysteine residues are uniformly replaced with tyrosine, phenylalanine, and alanine, respectively). The three-dimensional aqueous solution structures of the wild type and the active variant TPY4 reveal very similar beta-hairpin conformations. In contrast, the inactive variant TPA4 is unstructured in solution. The arrangement of the tyrosine side chains in the TPY4 structure suggests that the beta-hairpin is stabilized by aromatic ring stacking interactions. This is supported by experiments in which the beta-hairpin structure of TPF4 is disrupted by the addition of phenol, but not by the addition of an equimolar amount of cyclohexanol. We have also determined the structures of wild-type tachyplesin I and TPY4 in the presence of dodecylphosphocholine micelles. Both peptides undergo significant conformational rearrangement upon micelle association. Analysis of the micelle-associated peptide structures shows an increased level of exposure of specific hydrophobic side chains and an increased hydrophobic integy moment. Comparison of the structures in micelle and aqueous solution for both wild-type tachyplesin I and TPY4 reveals two requirements for high antimicrobial activity: a beta-hairpin fold in solution and the ability to rearrange critical side chain residues upon membrane association.

Capillary electrochromatographic separation of aromatic amino acids possessing peptides using porphyrin derivatives as the inner wall modifiers

Two different porphyrin derivatives (H2TPP(m-OPh)4 and Rh(III)TPP(m-OPh)4) were investigated with respect to their capability to help resolution of five model aromatic peptides in capillary electrophoresis/open tubular capillary electrochromatography. Though the main separation mechanism was preferentially based on the ionic properties of the separated analytes, involvement of particularly H2TTPP(m-OPh)4-peptide interactions at alkaline pH (8.0) was clearly demonstrated. In combination with Tris-phosphate buffer, a speed up of the separation was observed at pH 2.25 (particularly if Rh(III)TPP(m-OPh)4 was used as capillary coating); in spite of the speed up of the separation the selectivity of the system was sufficient and resulted in a complete separation of the five model peptides. It can be expected that Rh(III)TPP(m-OPh)4 capillary coating in combination with Tris-phosphate buffer can be generally used for a considerable speeding up of lengthy separations of peptides in acidic media with some decrease in the separation power of the system.

Profiling and screening analysis of 27 aromatic amino acids by capillary electrophoresis in dual modes

An efficient capillary electrophoretic (CE) profiling and screening system based on dual modes of capillary zone electrophoresis (CZE) and micellar electrokinetic capillary chromatography (MEKC) was developed for the simultaneous determination of 23 nonprotein amino acids (NPAAs) and 4 protein amino acids with aromatic moiety. It involves separation by an uncoated fused-silica capillary under phosphoric acid buffer in CZE mode and by another uncoated fused-silica capillary under neutral sodium dihydrogen phosphate buffer containing sodium dodecyl sulfate in MEKC mode. Migration orders of the amino acids studied on the two separation modes under each optimum condition were very different. The repeatability of migration times measured by the CZE and MEKC was found to be better than 4.8 and 3.4%, respectively, thereby enabling to cross-check the identification of each amino acid. The method linearity and limit of detection of the CZE for each amino acid were found to be adequate for the assay of aromatic amino acids. When the present CE profiling and screening analysis in dual modes was applied to plant seeds, NPAAs such as mimosine from Mimosa pudica Linné, and 2-phenylglycine from Lindera erythrocarpa Makino were positively detected along with tryptophan, phenylalanine and tyrosine.

[Spectral study of the microenviroment change of aromatic amino-acid residues in BSA induced by pH]

The microenvironment change of aromatic amino-acid residues in BSA at various pH were studied by fluorescence spectra and ultraviolet absorption spectra. It suggested that the change of protein surface and surface hydrophobicity from result. Compared to neutral pH, the Trp microenvironment seemed to be more hydrophobic at lower pH indicating less local surface hydrophobicity of BSA. At higher pH, the protein undergo conformational changes and unhold, the more buried Phe exposed to solvents consistent with stronger surface hydrophobicity of BSA.

[The application quantitative structure-retention relationship of GC to aid MS qualitative analysis]

In this paper, a method, based on the prediction of the Kovats retention indices of related polysubstituted alkylbenzenes from the indices of benzene, monsubstituted alkylbenzenes and disubstituted alkylbenzenes, was used to aid qualitative analysis with mass spectrometry alone. A disproportinated aromatic product and the basic compounds of alkylbenzene were analyzed with gas chromatography isothermally at 100 degrees C separately. In order to cut down the analysis time and increase the resolution, the disproportionated aromatic product was analyzed using temperature programming with gas chromatographymass spectrometry (GC-MS). The Kovats retention indices of the basic compounds were determined and those of the polysubstituted alkylbenzenes were predicted with the method which was proposed by us previously. The isomers of polysubstituted alkylbenzenes have similar mass spectra, so they can not be identified unambiguously by MS alone. For the differences of the Kovats retention index between isomers of polysubstituted alkylbenzenes are larger, it can be identified by matching the experimental retention indices with the predicted ones. The positional isomers of polysubstituted alkylbenzenes which are very difficult to be interpreted by MS alone have been identified explicitly.