Quantitative determination of secondary amines: measurement of N-methylalanine

A simple, rapid method for the quantitative estimation of secondary amines was developed based upon the reaction of this group of compounds with sodium nitroprusside and acetaldehyde. The conditions for optimal color production are described and the extent of interference by various primary and tertiary amines is evaluated. No appreciable interference from other compounds commonly found in biological tissues was found. This assay permits estimation of 0.05–0.80 μmoles of N-methylalanine. The possible application of this method to the measurement of proline and hydroxyproline is suggested.     

Mass spectrometry imaging: Towards a lipid microscope?

Biological imaging techniques are the most efficient way to locally measure the variation of different parameters on tissue sections. These analyses are gaining increasing interest since 20 years and allow observing extremely complex biological phenomena at lower and lower time and resolution scale. Nevertheless, most of them only target very few compounds of interest, which are chosen a priori, due to their low resolution power and sensitivity. New chemical imaging technique has to be introduced in order to overcome these limitations, leading to more informative and sensitive analyses for biologists and physicians.Two major mass spectrometry methods can be efficiently used to generate the distribution of biological compounds over a tissue section. Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry (MALDI-MS) needs the co-crystallization of the sample with a matrix before to be irradiated by a laser, whereas the analyte is directly desorbed by a primary ion bombardment for Secondary Ion Mass Spectrometry (SIMS) experiments. In both cases, energy used for desorption/ionization is locally deposited -some tens of microns for the laser and some hundreds of nanometers for the ion beam- meaning that small areas over the surface sample can be separately analyzed. Step by step analysis allows spectrum acquisitions over the tissue sections and the data are treated by modern informatics software in order to create ion density maps, i.e., the intensity plot of one specific ion versus the (x,y) position.Main advantages of SIMS and MALDI compared to other chemical imaging techniques lie in the simultaneous acquisition of a large number of biological compounds in mixture with an excellent sensitivity obtained by Time-of-Flight (ToF) mass analyzer. Moreover, data treatment is done a posteriori, due to the fact that no compound is selectively marked, and let us access to the localization of different lipid classes in only one complete acquisition.     

Malonichrome,a new iron chelate from Fusarium roseum

The predominant iron chelates, or siderochromes, produced by the fungus, Fusarium roseum during culture periods up to seven days are the ester type fusarinine compounds. During longer periods of incubation, the fusarinine compounds completely disappear from the culture medium and are replaced by a new siderochrome. The new compound has been isolated, purified, and its structure determined. It is a cyclic hexapeptide containing one residue of l-alanine, two residues of glycine and three residues of δ-N-hydroxyornithine. The hydroxylamino groups of the ornithine residues are acylated with 3 mol of malonic acid to form a negatively charged ferrichrome type chelate. The circular dichroism spectrum indicates that the stereochemistry about the iron is Λ-cis. This compound, which we name malonichrome, is not an efficient iron donor to F. roseum nor does it show growth factor activity towards Arthrobacter flavescens.     

纳米二次离子质谱技术(NanoSIMS)在微生物生态学研究中的应用

超高分辨率显微镜成像技术与同位素示踪技术相结合的纳米二次离子质谱技术(NanoSIMS)具有较高的灵敏度和离子传输效率、极高的质量分辨率和空间分辨率(＜ 50 nm),代表着当今离子探针成像技术的最高水平.利用稳定性或者放射性同位素在原位或者微宇宙条件下示踪目标微生物,然后将样品进行固定、脱水、树脂包埋或者导电镀膜处理,制备成可供二次离子质谱分析的薄片,进一步通过NanoSIMS成像分析,不仅能够在单细胞水平上提供微生物的生理生态特征信息,而且能够准确识别复杂环境样品中的代谢活跃的微生物细胞及其系统分类信息,对于认识微生物介导的元素生物地球化学循环机制具有重要意义.介绍了纳米二次离子质谱技术的工作原理和技术路线,及其与同位素示踪技术、透射电子显微镜(TEM)、扫描电子显微镜(SEM)、荧光原位杂交技术(FISH)、催化报告沉积荧光原位杂交技术(CARD-FISH)、卤素原位杂交技术(Halogen In Situ Hybridization,HISH)等联合使用在微生物生态学研究方面的应用.     

Reaction of sodium hypochlorite with amines and amides: a new method for quantitating amino sugars in monomeric form

Free and N-acetylated hexosamines can be determined spectrophotometrically by a three-stage assay: chlorinating the amide or amine with NaOCl; reducing unreacted NaOCl with NaNO₂; and reacting chloroamide (-amine) with amylose-KI reagent to produce the blue amylosetriiodide complex, measured at 615 nm. Distinctive behavior of the common 2-amino-2-deoxy-d-hexoses and their 2-acetyl derivatives allows three types of measurements to be made: (a) identification and differentiation by characteristic behavior (assay individually in primary cacodylate buffers over the pH range 6.0–9.5, then adjust pH to 5.5 with secondary phthalate buffer and remeasure the color); (b) assay individually in a single buffer at the optimum pH; and (c) assay differently admixed 2-amino-2-deoxy-d-hexose · HCl and 2-acctamindo-2-deoxy-d-hexose (assay in primary buffer at pH 9.0–9.5 gives measure of only HexNAc (no reaction with ManNAc), then adjust pH to 5.5 with secondary buffer to measure additional color that results only from HexN · HCl).     

A Pipeline for Screening Small Molecules with Growth Inhibitory Activity against Burkholderia cenocepacia

Infections with the bacteria Burkholderia cepacia complex (Bcc) are very difficult to eradicate in cystic fibrosis patients due the intrinsic resistance of Bcc to most available antibiotics and the emergence of multiple antibiotic resistant strains during antibiotic treatment. In this work, we used a whole-cell based assay to screen a diverse collection of small molecules for growth inhibitors of a relevant strain of Bcc, B. cenocepacia K56-2. The primary screen used bacterial growth in 96-well plate format and identified 206 primary actives among 30,259 compounds. From 100 compounds with no previous record of antibacterial activity secondary screening and data mining selected a total of Bce bioactives that were further analyzed. An experimental pipeline, evaluating in vitro antibacterial and antibiofilm activity, toxicity and in vivo antibacterial activity using C. elegans was used for prioritizing compounds with better chances to be further investigated as potential Bcc antibacterial drugs. This high throughput screen, along with the in vitro and in vivo analysis highlights the utility of this experimental method to quickly identify bioactives as a starting point of antibacterial drug discovery.     

A new colorimetric assay for glutathione transferase-catalyzed halogen ion release for high-throughput screening

Glutathione transferases (GSTs; EC 2.5.1.18) form a group of multifunctional enzymes catalyzing the conjugation of a broad range of toxicologically important halogenated compounds to the tripeptide glutathione (GSH) with concomitant halogen ion release. In the present work, a rapid quantitative screening method for GSTs based on colorimetric measurement of halogen ions released from halogenated xenobiotics was developed. The assay is based on the color formation resulting from the reaction of Hg(SCN)₂ with the released halogen ion of the substrate in the presence of Fe³⁺. The color intensity is proportional to the extent of the catalytic reaction, allowing a quantitative measurement of the GST catalytic activity. The assay can be performed using purified recombinant enzyme (the isoenzyme GmGSTU4-4 from Glycine max) or crude recombinant Escherichia coli cell lysates in 96-well microtiter plates. The suitability of the colorimetric assay for screening mutant GST variants derived from a directed evolution library was successfully evaluated. In addition, the assay was also used for screening GST synthetic inhibitors. It was concluded that the proposed colorimetric assay is selective and sensitive and allows the screening of large numbers of samples within a few minutes.     

Primary Ion Depletion Kinetics (PIDK) Studies as a New Tool for Investigating Chemical Ionization Fragmentation Reactions with PTR-MS

We report on a new approach for studying fragmentation channels in Proton Transfer Reaction-Mass Spectrometry (PTR-MS), which we name primary ion depletion kinetics (PIDK). PTR-MS is a chemical ionization mass spectrometric (CIMS) technique deploying hydronium ions for the chemical ionization. Induced by extremely high concentrations of analyte M, depletion of the primary ions in the drift tube occurs. This is observed as quasi zero concentration of the primary ion H₃O⁺, and constant MH⁺. Under these non-standard conditions, we find an overall changed fragmentation. We offer two explanations. Either the changed fragmentation pattern is the result of secondary proton transfer reactions. Or, alternatively, the fast depletion of H₃O⁺ leads to reduced heating of H₃O⁺ in the drift field, and consequently changed fragmentation following protonation of the analyte M. In any case, we use the observed changes in fragmentation as a successful new approach to fragmentation studies, and term it primary ion depletion kinetics, PIDK. PIDK easily yields an abundance of continuous data points with little deviation, because they are obtained in one experimental run, even for low abundant fragments. This is an advantage over traditional internal kinetic energy variation studies (electric field per number density (E/N) variation studies). Also, some interpretation on the underlying fragmentation reaction mechanisms can be gleamed. We measure low occurring fragmentation (<2% of MH⁺) of the compounds dimethyl sulfide, DMS, a compound that reportedly does not fragment, diethyl sulfide DES, and dipropyl sulfide DPS. And we confirm and complement the results with traditional E/N studies. Summing up, the new approach of primary ion depletion kinetics allows for the identification of dehydrogenation [MH⁺ -H₂] and adduct formation (RMH⁺) as low abundant fragmentation channels in monosulfides.     

Enhancement of protonated molecular ions and ammonium·molecular ion complexes in direct-liquid-introduction-mass spectrometry of carbohydrates

Addition of ammonium acetate to the mobile phase in direct-liquid-introduction mass spectrometry enhances the abundance of the protonated molecular ion or ammonium·molecular ion complex for compounds of biological interest. The efficacy of the method was investigated by comparing mass spectra obtained, with and without ammonium acetate, for a variety of underivatized, per-O-acetylated, and per-O-alkylated carbohydrates, and for several underivatized peptides. The mass spectra of the per-O-alkylated carbohydrates obtained by direct-liquid-introduction mass spectrometry with ammonium acetate were also compared to those obtained by thermospray mass spectrometry.     

Regioselective O-deacylation of fully acylated glycosides and 1,2-O-isopropylidenealdofuranose derivatives with hydrazine hydrate

On hydrazinolysis in 1:4 acetic acid-pyridine, and in pyridine, partial O-deacylation of fully acylated methyl glycosides and some other glycosyl compounds (23 compounds) was found to be induced, to give, in good yields, products bearing one free hydroxyl group; the results obtained indicated that, among the primary and secondary O-acyl groups, the 2-O-acyl groups were, in general, the most labile toward the nucleophile (hydrazine). Hydrazinolysis of 1,2-O-isopropylidenealdofuranose acylates (3 compounds), on the other hand, gave, in high yield, the corresponding monoacyl derivatives having the protecting group on their primary hydroxyl group. The factors possibly involved in the regioselectivity of the hydrazinolysis were discussed.     

On the specificity of the folin and lowry reagents for amine derivatives.

Reactivities of several amine derivatives with the Folin and Lowry reagents were examined. Tertiary amines reacted with the Folin reagent to produce a blue color, and secondary amines having a 2-hydroxyethyl group reacted with the Folin reagent only in the presence of Cu²⁺, i.e., with the Lowry reagent. On the other hand, primary and quarternary amines and amine N-oxides produced no color with either reagent. Reactivities of tertiary amines were greatly influenced by the nature of the N-substituted groups, and the color yield of those forming stable chelate complexes with metals was strongly inhibited by the presence of Cu²⁺, indicating that the formation of a stable complex with Cu²⁺ reduces the reactivity of tertiary amino nitrogen. The requirement of Cu²⁺ for the color development with secondary amines having a 2-hydroxyethyl group may be due to the formation of weak chelate complex with Cu²⁺.     

When Do Short-Wave Cones Signal Blue or Red? A Solution Introducing the Concept of Primary and Secondary Cone Outputs

A recent paper by Oh and Sakata investigates the “incompletely solved mystery” of how the three cone responses map onto perceived hue, and particularly the S cone’s well-known problematic contribution to blueness and redness. Citing previous workers, they argue the twentieth century traditional multistage model does not satisfactorily account for color appearance. In their experiment, increasing S cone excitation with shortening wavelength from about 480–460 nm increased perceived blueness up to the unique Blue point at 470 nm, when (a) it began decreasing and (b) redness perception began increasing. The authors asked, What mechanism can be responsible for such functions? I demonstrate a solution. First, it is shown the problem does not lie in the traditional opponent color chromatic responses yellow-blue, red-green (y-b, r-g, which accurately predict the above functions), but in the traditional multistage model of mapping cone responses to chromatic response functions. Arguably, this is due to the S cone’s hypothetically signaling both blueness and redness by the same mechanism rather than by different, independent, mechanisms. Hence a new distinction or mechanism is proposed for a more accurate model, that introduces the new terms primary and secondary cone outputs. However, this distinction requires that the cones S, M, L each directly produce one of the three spectral chromatic responses b, g, y. Such a model was recently published, based on extremely high correlation of SML cone responsivities with the three spectral (bgy) chromatic responses. This model encodes the former directly onto the latter one-to-one as cone primary outputs, whilst S and L cones have a further or secondary function where each produces one of the two spectral lobes of r chromatic response. The proposed distinction between primary and secondary cone outputs is a new concept and useful tool in detailing cone outputs to chromatic channels, and provides a solution to the above “incompletely solved mystery.” Thus the S cone has a primary output producing the total b chromatic response and a secondary output that shares with the L cone the production of r chromatic response, thus aligning with Oh and Sokata’s results. The model similarly maps L cone to yellowness as primary output and to redness as secondary output.     

Detection of fungal infestations of wood by ion mobility spectrometry

During their growth on wood many fungi produce characteristic volatile organic compounds as secondary metabolites. These microbial volatile organic compounds (MVOCs) can be used as indicators of fungal growth even when such growth is concealed. In order to investigate the formation of these volatile metabolites on building materials, specimens of pine sapwood on agar media colonized by the dry-rot fungus Serpula lacrymans and a mixture of six moulds were examined. MVOCs from this fungal growth were studied over a period of up to half a year by ion mobility spectrometry (IMS) headspace analysis using a sensitive, portable IMS mini-device. The IMS headspace spectra from the growing fungal specimens obtained during this time span are differed from non-incubated wood specimens and indicate the presence of a mixture of MVOCs. The composition and amount of volatile metabolites of the fungi changed during cultivation. This was confirmed by a principal component analysis (PCA). Identification of different MVOCs in the headspace according to drift time and the mobility of ionized gaseous species in reference to GC-MS investigations were proposed. It was concluded that IMS can be used as a rapid and sensitive on-site method to indicate actively growing fungi concealed within wood.     

Interaction of an ion beam with the target in electron microscope applications

When based on the power-potential law of Lindhard et al. (Mat. Fys. Dan. Vid. Selsk, 33: 1–42, 1963) for ionic impact phenomena on the surfaces of a target, the universal curves of nuclear and electronic energy loss-energy, their resulting yield-energy relationships of sputtering and secondary electron emission yield-energy and range-energy have consistently been derived.According to the results obtained from the above experimental data, a diffusion model of an ion beam penetrating a target is proposed, which takes place throughout a hemisphere with its centre located at half the diffusion depth, and which is found to agree well with the empirical data of ion beam penetration, energy-dissipation profiles and the backscattering coefficient as a function of the reduced depth.Owing to the diffusion model's data, the total secondary electron emission yield due to both primary and backscattering ions is obtained. More importantly, radiation damage in ion beam applications is consistently evaluated as a function of the reduced energy ratio.     

Colorimetric determination of catechol siderophores in microbial cultures

A highly sensitive spectrophotometric method for the selective detection of catechol compounds such as catechol siderophores (e.g., enterobactin) is described. The basis of the method involves the ability of the vicinal aromatic hydroxyl groups under acidic conditions to bring about a reduction of Fe3+ (from ferric ammonium citrate) to Fe2+. Detection of Fe2+ in the presence of Fe3+ is made with 1,10-phenanthroline under previously established conditions. The assay mixture is heated at 60 degrees C for 1 h to accelerate the development of color which is subsequently measured at 510 nm. The Beer-Lambert law is obeyed over the range of 0.16 to 60 microM 2,3-dihydroxybenzoic acid. Compared to the Arnow nitration method, the assay is more responsive, is approximately seven times more sensitive, and is effective with catechols substituted at positions 3 and 4. The method gives positive results with catechols such as DL-DOPA, L-dopamine, (+/-)-epinephrine, and DL-norepinephrine. Very rapid color development is obtained with ascorbic acid and p-diols, while m-diols are poorly detected. Low degrees of reactivity are shown by hydroxylamino and hydroxamate compounds. Phenolic, sulfydryl, indolyl, and quinonyl derivatives do not interfere with the reaction. The method has been adapted to determine catechol compounds in the culture medium of bacterial cells grown at different iron concentrations.     

Secondary ion mass spectrometry (SIMS) of standards for analysis of soft biological tissue.

Gelatin films containing water-soluble salts of lithium, rubidium, strontium, or copper were analyzed by secondary ion mass spectrometry. Calcium and vanadium organometallic compounds in an epoxy resin were similarly analyzed. A linear relationship between positive secondary ion intensity and ion concentration was observed over several decades of ion concentration and at absolute concentrations as low as 1 wt ppm. These standards can be used for quantitative analysis of tissue or other biological material in epoxy resins, providing a highly sensitive method for simultaneous quantitation and localization of elements.     

Characterization of Bacteria by Particle Beam Mass Spectrometry

A technique is described for detecting and characterizing bacteria on a single-particle basis by mass spectrometry. The method involves generation of a particle beam of single whole cells which are rapidly volatilized and ionized in vacuum in the ion source of a quadrupole mass spectrometer. The particle beam can be generated, with minimal sample handling, from a naturally occurring aerosol or from a solution of bacteria that can be dispersed as an aerosol. The mass spectrum is generated by successively measuring the average intensities of different mass peaks. The average intensity is obtained by measuring the ion intensity distribution at the particular mass (m/e) for ion pulses from more than 1,000 bacteria particles. Bacillus cereus, Bacillus subtilis, and Pseudomonas putida samples were analyzed to test the capability of the instrument for differentiating among species of bacteria. Significant ion-intensity information was produced over the m/e range of 50 to 300, an improvement over previous pyrolysis-mass spectrometry results. The complex mass spectra contained a few unique peaks which could be used for the differentiation of the bacteria. A statistical analysis of the variations in peak intensities among the three bacteria provided a quantitative measure of the reproducibility of the instrument and its ability to differentiate among bacteria. The technique could lead to a new rapid method for the analysis of microorganisms and could be used for the detection of airborne pathogens on a continuous, real-time basis.     

Soft-sensor assisted dynamic investigation of mixed feed bioprocesses

Recombinant mixed feed bioprocesses are characterized by the controlled feeding of multiple defined carbon sources aiming at increased productivities. However, mixed feed process design is challenging due to physiological constraints such as adaptation times and catabolite repression.A novel soft-sensor assisted dynamic method that allows the science-based process design with respect to co-utilization of primary and secondary substrate was developed. The method is based on the control of the specific uptake rates of primary and secondary substrate via a combination of a rate-based soft sensor and in-line infrared spectroscopy. Maximum secondary substrate specific uptake rates and adaptation times are determined by a combination of dynamic pulse and ramp experimentation.The power of the presented method was demonstrated on a recombinant Escherichia coli pBAD mixed feed process with d-glucose as primary and l-arabinose as secondary carbon source. Onset of catabolite repression was observed once a total specific substrate uptake rate of 1.0 g/gh was exceeded. Adaptation times to l-arabinose were determined as ～10 min.The presented method can be considered generically applicable for the physiological investigation of mixed feed systems. Furthermore, metabolic capabilities of the promising but yet unexplored E. coli pBAD mixed feed system were explored for the first time.