Homochirality and life

Before the emergence of life, left-handed amino acids (L-enantiomers) were selected and right-handed amino acids (D-enantiomers) were eliminated on the primal earth. Nevertheless, with the progress of analytical methods, D-amino acids have recently been found in higher order living organisms in the form of free amino acids, peptides, and proteins. Free D-amino acids have numerous physiological functions. D-amino acids containing animal peptides are well known as opioid peptides. D-amino acids in protein are related to aging. In this review, we describe the D-amino acids that are present and function as D-amino acid biosystems in our bodies.     

Basic profiles of organic acids in urine

Altogether 143 of the organic acids regularly occurring in urine of healthy individuals are identified as methyl esters by gas chromatography-mass spectrometry with respect to their complete chemical structures. They are classified as dicarboxylic acids, oxocarboxylic acids, hydroxycarboxylic acids, aromatic acids, furancarboxylic acids, nitrogen-containing acids and acid conjugates. By pre-fractionating the complex mixture of the total organic acids, peak overlap is minimized, and substances in low concentrations can also be detected and identified. The qualitative patterns of the urinary organic acids in the fractions are constant and reproducible, and in many cases a reliable identification of organic acids is possible by gas chromatography alone, using methylene units and separation on OV-1701 capillary columns.     

Simultaneous quantitation of Krebs cycle and related acids by mass fragmentography

Methods are described for simultaneous quantitation of Krebs cycle and related acids by gas chromatography--mass spectrometry using deuterium-labelled acids and n-butyl-d9-esters of the organic acids as internal standards. Using sulphuric acid as esterification catalyst, only lactic, succinic, fumaric, malic, maleic and citric acids were found to be stable to hydrogen exchange and could be used as reference standards in the deuterated form. In contrast, pyruvic, oxalacetic, alpha-ketoglutaric and malonic acids were found to exchange their deuterium readily and could not be employed for this purpose. All the acids could be quantitated using n-butyl-d9-esters of reference organic acids as internal standards, following a separate preparation of the n-butyl derivatives of the unknown acids. The method is suitable for routine analysis of organic acids at the picogram level in perchloric acid extracts of tissues.     

Determination of absolute configurations of amino acids by asymmetric autocatalysis of 2-alkynylpyrimidyl alkanol as a chiral sensor

Asymmetric autocatalysis of 2-alkynyl-5-pyrimidyl alkanol is employed as a chiral sensor of 20 amino acids. Asymmetric autocatalysis using amino acids as chiral initiators gave pyrimidyl alkanols of the absolute configurations that were correlated with those of the amino acids. The enantiomeric excesses of pyrimidyl alkanol are invariably high even when the enantiomeric excess of amino acids is as low as 0.1%. Thus, by determining the absolute configuration of pyrimidyl alkanol with high enantiomeric excess, one can determine the absolute configuration of amino acids even when their enantiomeric excess is low.     

New Naturally Occurring Amino Acids

The majority of the 500 or so naturally occurring amino acids known today were discovered during the last 30 years, for example during the search for new antibiotics in the culture media of microorganisms, or as components of the antibiotics in fungi, seeds, in numerous plants and fruits, and in the body fluids of animals. Some 240 of these amino acids occur free in nature, some only as intermediates in metabolism. This article provides an overview of the developments that have taken place in this area since 1956 when the last review appeared. Summary accounts are presented, dealing with new unsaturated amino acids, cyclopropane- and cyclobutane-amino acids, heterocyclic amino acids, halogen-containing amino acids sulfur-, selenium- and phosphorus-containing amino acids as well as aliphatic amino acids. In a few cases, e. g. betalamic acid and muscaflavin, the biosynthesis is described in detail.     

Imaging mass spectrometry with silver naeoparticles reveals the distribution of fatty acids in mouse retinal sections

A new approach to the visualization of fatty acids in mouse liver and retinal samples has been developed using silver nanoparticles (AgNPs) in nanoparticle-assisted laser desorption/ ionization imaging mass spectrometry (nano-PALDI-IMS) in negative ion mode. So far, IMS analysis has concentrated on main cell components, such as cell membrane phospholipids and cytoskeletal peptides. AgNPs modified with alkylcarboxylate and alkylamine were used for nano-PALDI-IMS to identify fatty acids, such as stearic, oleic, linoleic, arachidonic, and eicosapentaenoic acids, as well as palmitic acid, in mouse liver sections; these fatty acids are not detected using 2,5-dihydroxybenzoic acid (DHB) as a matrix. The limit of detection for the determination of palmitic acid was 50 pmol using nano-PALDI-IMS. The nano-PALDI-IMS method is successfully applied to the reconstruction of the ion images of fatty acids in mouse liver sections. We verified the detection of fatty acids in liver tissue sections of mice by analyzing standard lipid samples, which showed that fatty acids were from free fatty acids and dissociated fatty acids from lipids when irradiated with a laser. Additionally, we applied the proposed method to the identification of fatty acids in mouse retinal tissue sections, which enabled us to learn the six-zonal distribution of fatty acids in different layers of the retina. We believe that the current approach using AgNPs in nano-PALDI-IMS could lead to a new strategy to analyze basic biological mechanisms and several diseases through the distribution of fatty acids.     

LC Determination of Trace Short-Chain Organic Acids in Wheat Root Exudates Under Aluminum Stress

A novel and reliable high-performance liquid chromatographic method for trace short-chain organic acids measurement in wheat root exudates under aluminum stress has been optimized and validated. The chromatographic separation of the short-chain organic acids (citric, oxalic, malonic, succinic, tartaric, malic, and acetic acids) was achieved with Bio-rad Aminex HPX-87H cation exchange resin column. These seven organic acids were identified and quantified in 25 min. Well-shaped peaks were obtained for trace organic acids using dilute sulfuric acid as mobile phase. Under optimum conditions, Bio-rad Aminex HPX-87H column showed distinct advantages of the ability to well separate different short-chain organic acids (especially for tartaric and malic acids, as well as malonic and acetic acids) in wheat root exudates under aluminum stress, and offered accurate and precise results for the analysis of these organic acids. This HPLC method can efficiently eliminate the aluminum’s interference and is quite suitable to the trace detection of trace organic acids in wheat root exudates under aluminum stress.     

LC Determination of Trace Short-Chain Organic Acids in Wheat Root Exudates Under Aluminum Stress

A novel and reliable high-performance liquid chromatographic method for trace short-chain organic acids measurement in wheat root exudates under aluminum stress has been optimized and validated. The chromatographic separation of the short-chain organic acids (citric, oxalic, malonic, succinic, tartaric, malic, and acetic acids) was achieved with Bio-rad Aminex HPX-87H cation exchange resin column. These seven organic acids were identified and quantified in 25 min. Well-shaped peaks were obtained for trace organic acids using dilute sulfuric acid as mobile phase. Under optimum conditions, Bio-rad Aminex HPX-87H column showed distinct advantages of the ability to well separate different short-chain organic acids (especially for tartaric and malic acids, as well as malonic and acetic acids) in wheat root exudates under aluminum stress, and offered accurate and precise results for the analysis of these organic acids. This HPLC method can efficiently eliminate the aluminum’s interference and is quite suitable to the trace detection of trace organic acids in wheat root exudates under aluminum stress.

     

Simultaneous determination of C2-C22 non-esterified fatty acids and other metabolically relevant carboxylic acids in biological material by gas chromatography of their benzyl esters

A method for the simultaneous determination of non-esterified short-, medium- and long-chain fatty acids and other types of metabolically relevant carboxylic acids such as hydroxy, keto, aromatic and dicarboxylic acids in biological material by capillary gas chromatography of benzyl ester derivatives is described. Sample preparation avoiding incomplete isolation of carboxylic acids consisted of deproteinization and extraction with ethanol, fixation of carboxylic acids as carboxylates, removal of interfering compounds such as neutral lipids by hexane extraction and amino acids, acyl carnitines and other cations by cation-exchange chromatography, derivatization of keto groups of ketocarboxylic acids into O-methyl oximes and benzyl ester formation by reaction of the potassium carboxylates with benzyl bromide via crown ether catalysis. The sample preparation conditions were investigated, showing the usefulness of this method for quantitative determinations. Chromatograms obtained from human serum, human urine and rat heart ventricle and concentrations of carboxylic acids in these specimens are presented.     

Measurement of polyunsaturated fatty acids of myocardial lipids by high performance liquid chromatography

Summary This report describes a modified method for the separation and analysis of polyunsaturated fatty acids such as 20:4, 20:5, and 22:6, using HPLC. The results show that these fatty acids are well separated from the saturated acids. Since the unsaturated fatty acids elute earlier than saturated acids, and this method does not require the fractionation of free fatty acids using thin layer chromatography, a necessary step for the gas chromatographic analysis, the recoveries of polyunsaturated fatty acids were significantly higher as compared to those from gas chromatography. Furthermore, HPLC and gas chromatographic methods gave identical results for the acyl chain composition of phosphatidylserine. The advantages of using HPLC over gas chromatography in determining the acyl chain composition of free fatty acids and phospholipids are also discussed.     

Analysis of amino acids as formamidene butyl esters by electrospray ionization tandem mass spectrometry.

Amino acid formamidene butyl esters are optimally prepared by heating amino acids with dimethylformamide dimethylacetal (DMF-DMA) for 2 minutes at 65 degrees C and then with n-butanol/hydrogen chloride for 15 minutes at 65 degrees C. The formamidene butyl esters of simple alpha-amino acids and beta-amino acids afford between 1.1 and 20 times the signal intensity of the corresponding butyl esters during electrospray ionization tandem mass spectral analysis. Complex alpha-amino acids, such as ornithine, arginine and citrulline, and gamma-amino acids are better analyzed as butyl esters. Secondary alpha-amino acids, such as proline and sarcosine, give a mixture of two iminium salts with the DMF-DMA derivatization method. A derivative incorporating two molecules of the amino acid predominates at higher derivatization temperatures. Contrary to a previous report, N-formylamino acids were not detected. The presence of secondary amino acids in amino acid mixtures, derivatized as formamidene butyl esters, affords derivatives that incorporate two different amino acids. The new formamidene butylation method is unlikely to replace the butylation procedure used by neonatal blood spot screening programs for amino acid disorders, since a much poorer response was obtained with formamidene butyl esters of arginine and citrulline, important in the diagnosis of arginase deficiency and citrullinaemia.     

Micelles for signal enhancement and novel selectivity of dansyl amino acids

Fluorescence intensity of various chemical species is enhanced in the microenvironment provided by micelles. Parameters which affect fluorescence intensities are examined by using dansyl (Dns) amino acids as the probe. The retention behavior of Dns-amino acids in micellar LC is examined by using ion-exchange-induced stationary phases. The type and concentration of micellar agent and modifier ion as well as concentration of acetonitrile in the mobile phase affect the retention and signal intensity of Dns-amino acids. The order of elution of Dns-amino acids obtained with the micellar mobile phase is very different from that observed in conventional reversed-phase LC. Fluorescence intensities of Dns-amino acids are enhanced by the micellar mobile phase.     

错配核酸的研究进展

本文通过介绍多种错配核酸的结构及其热力学性质，详细地描述了非Watson-Crick配对核酸的最新进展。这方面的研究有利于阐明生物体内错配核酸的识别修复机理及核酸二级结构的预测，并为合理设计新的人工核酸修复酶提供了理论基础。     

Ligand-exchange chromatography of amino acids on nickel-Chelex 100.

A ligand-exchange chromatographic proceudre for the selective separation of amino acids from inorganic ions is presented. It was found that the binding of amino acids to the nickel-Chelex 100 resin is pH dependent. At pH 8.5-9.1, only the basic amino acids lysine, histidine and arginine are quantitatively attached to the complex, whereas at pH 11, other amino acids with the exception of aspartic acid and glutamic acid are also bound, although not quantitatively. All of the amino acids can be eluted from the complex with 3 M ammonia solution without the displacement of nickel ions from the complex. This method can be used for the removal of the basic amino acids from solutions in the presence of inorganic ions as well as other amino acids.     

Amino acids as chiral selectors in enantioresolution by liquid chromatography

Amino acids are unique in terms of their structural features and multidimensional uses. With their simple structures and the ready availability of both enantiomers, amino acids not only serve as a chiral pool for synthesis but also provide an inexpensive pool for resolution studies. There has been no attempt to review the application of amino acids as chiral selectors for chromatographic enantioresolution of pharmaceuticals and other compounds. The present paper deals with application of l-amino acids and complexes of l-amino acids with a metal ion, particularly Cu(II), as an impregnating reagent in thin-layer chromatography or as a chiral ligand exchange reagent or a chiral mobile phase additive in both thin-layer chromatography and high-performance liquid chromatography. Enantiomeric resolution of β-blockers, nonsteroidal anti-inflammatories, amino acids (and their derivatives) and certain other compounds is discussed.     

Protein alignment: Exact versus approximate. An illustration

We illustrate solving the protein alignment problem exactly using the algorithm VESPA (very efficient search for protein alignment). We have compared our result with the approximate solution obtained with BLAST (basic local alignment search tool) software, which is currently the most widely used for searching for protein alignment. We have selected human and mouse proteins having around 170 amino acids for comparison. The exact solution has found 78 pairs of amino acids, to which one should add 17 individual amino acid alignments giving a total of 95 aligned amino acids. BLAST has identified 64 aligned amino acids which involve pairs of more than two adjacent amino acids. However, the difference between the two outputs is not as large as it may appear, because a number of amino acids that are adjacent have been reported by BLAST as single amino acids. So if one counts all amino acids, whether isolated (single) or in a group of two and more amino acids, then the count for BLAST is 89 and for VESPA is 95, a difference of only six. © 2015 Wiley Periodicals, Inc.     

Profiling and characterisation by liquid chromatography/multi-stage mass spectrometry of the chlorogenic acids in Gardeniae Fructus

The chlorogenic acids of Gardeniae Fructus used traditionally as a Chinese herbal medicine (zhizi) have been investigated qualitatively by liquid chromatography/multi-stage mass spectrometry (LC/MS(4)). Twenty-nine chlorogenic acids were detected and twenty-five characterised to regioisomer level on the basis of their fragmentation, twenty-four for the first time from this source. Assignment to the level of individual regioisomers was possible for three caffeoylquinic acids, three dicaffeoylquinic acids, three sinapoylquinic acids, four caffeoyl-sinapoylquinic acids, two feruloyl-sinapoylquinic acids, one p-coumaroyl-sinapoylquinic acid, three (3-hydroxy, 3-methyl)glutaroylquinic acids, two (3-hydroxy, 3-methyl)glutaroyl-feruloylquinic acids, one (3-hydroxy, 3-methyl)glutaroyl-dicaffeoylquinic acid, and one (3-hydroxy, 3-methyl)glutaroyl-caffeoyl-feruloylquinic acid. Six (3-hydroxy, 3-methyl)glutaroyl-caffeoylquinic acids were detected and two were tentatively assigned as 3-caffeoyl-4-(3-hydroxy, 3-methyl)glutaroylquinic acid and 3-caffeoyl-5-(3-hydroxy, 3-methyl)glutaroylquinic acid. The (3-hydroxy, 3-methyl)glutaroyl residue modifies the mass spectral fragmentation behavior and elution sequence compared with the chlorogenic acids that contain only a cinnamic acid residue(s). Fourteen of these twenty-nine chlorogenic acids have not previously been reported from any source.     

2-methoxyethanol as a solvent for conductometric acid-base titrations

Conductometric titrations of a series of organic acids in 2-methoxyethanol were performed with 1,3-diphenylguanidine (DPG) as titrant. For benzoic, p-chlorobenzoic and picric acids, phenylphenol and barbital, excellent recoveries were obtained from well-defined conductance vs. volume plots. Results for the dicarboxylic phthalic and adipic acids were also good. However, the titration curves for the difunctional salicylic and p-hydroxybenzoic acids were not clearly defined. The results are discussed and compared with cnductometric titrations of acids in other non-aqueous solvents. Several determinations of electrolyte conductance as a function of concentration revealed that, as expected, the selected substances are weak electrolytes in methoxyethanol.     

Gas chromatographic determination of pollutants in the chlorination and caustic extraction stage effluent from the bleaching of a bamboo pulp

The gas chromatographic detection and quantitative determination of various chlorophenolics as well as resin and fatty acids have been carried out in the chlorination and caustic extraction stage effluents generated in the laboratory by bleaching a bamboo pulp. A number of chlorinated phenols, catechols, guaiacols, syringaldehydes and resin acids as well as non-chlorinated saturated and unsaturated fatty acids together with resin acids have been detected. The concentration of various compounds detected have also been compared with the reported (96)LC(50) values.     

Analysis of Organic Acids in Physiological Fluids by High Performance Liquid Chromatography

Abstract

Most organic acids in physiological fluids are carboxylic acids or their glycine or glucuronide conjugates. Also included are hydroxyl compounds, such as phenols or cresols. By definition, compounds with a primary amino group, detectable by conventional amino acid analysers, are excluded. Organic acids are produced continuously in the body as intermediates in the metabolism of amino acids, carbohydrates and fats, and of drugs and food additives. They do not accumulate in the body, since they are rapidly converted to non-acidic end products or excreted as water soluble metabolites i n urine. However, if they are produced in excess, or if their metabolism is prevented by an inherited enzyme defect, concentrations increase in the tissues, blood and urine. Examples of excessive production are during fasting ketosis, in which acetoacetic and 3-hydroxybutyric acids and a range of dicarboxylic acids derived from breakdown of fatty acids accumulate, and lactic acidosis, secondary to hypoxia, when increases in lactic, pyruvic and 2-hydroxybutyric acids are common.