Fates of dissolved free amino acids in groundwater discharged through stream bed sediments

Laboratory simulations were used to investigate the immobilization of dissolved free amino acids (DFAAs) from groundwater discharged up through cores of stream-bed sediments from a first order stream. At natural concentrations, 99% of DFAAs supplied in groundwater were immobilized, with 14–25% of this material respired and the remainder retained in the lower layers of the cores (depth = 7.5 cm). Immobilization efficiencies increased with increasing groundwater DFAA concentrations and discharge rates. Moderate enrichments (up to 1 mg l^–1) appeared to stimulate biotic immobilization of DFAAs, while abiotic processes accounted for much of the increased immobilization at higher enrichments (tested up to 100 mg l^–1). Variability in groundwater discharge rates induced no changes in the proportional contribution of biotic and abiotic immobilization processes. Thus relative contributions of DFAA concentration and groundwater discharge rate to a given DFAA load (concentration × discharge rate) influenced the degree to which immobilized DFAAs were retained (as microbial biomass or adsorbed to the biofilm) or respired. Results showed that DFAAs in groundwater discharged through the stream-bed are in a highly dynamic state of flux, suggesting that these compounds may be more significant to the transfer of organic matter to the benthic trophic structure than their normally low concentrations in groundwater would imply.     

Free amino acids in some sponges

Most invertebrates, particularly those of marine origin, have relatively high concentrations of free amino acids which are considered an important constituent of their osmoregulatory mechanisms [1]. Very little information is available on the free amino acid distribution in Porifera [2,3]. Common amino acids in some sponges were recognised by paper chromatography by Inskip and Cassidy [4] and Ackermann et al. [5,6] included a few sponges in their survey of the occurence of nitrogen compounds in marine invertebrates. More recently Bergquist and Hartman [7] surveyed semiquantitatively the distribution of free amino acids in several sponges. In the present paper we report on the amino acid composition of 12 species of sponges belonging to the class Demospongiae as a part of a study on the metabolites of Porifera [8]. Fresh sponges were extracted with aqueous ethanol. The organic solvent was removed and the aqueous solution, after removal of the ether soluble compounds, was separated into cationic, anionic and neutral fractions by ion-exchange chromatography. The cation fraction was analysed for amino acids using an automatic amino acid analyser. The results, which are presented in Table 1, show that all species of sponges examined have a similar composition in common amino acids. Glycine almost always appears as the dominant protein amino acid, followed by high concentrations of alanine and glutamic acid, whereas relatively lower concentrations of basic amino acids are present. In Axinella cannabina, Chondrosia reniformis, Chondrilla nucula, Cliona viridis and Hymeniacidon sanguinea, glycine represents more than 77% of the total amino acids. The high percentage of free glycine (90.4%) in Chondrosia reniformis is noteworthy. The anionic and the neutral fractions were examined for sulfur-containing amino acids using PC. Taurine (Table 2) was detected in all the Porifera examined; this is in agreement with previous observations [5–7]. N-Methyltaurine was identified in some of the species examined, whereas neither N,N-dimethyltaurine nor N,N,N-trimethyltaurine were found.     

Gradient of dissolved free amino acids and phytoplankton in a shallow bay

A 3 h survey of the concentrations of individual free amino acids, chlorophyll a and phytoplankton species biomass was conducted in the surface waters of a shallow bay. Significant coefficients of correlation were found between chlorophyll a, nanoflagellates, and DFAA concentrations. Although phytoplankton biomass variations sometimes relate to DFAA concentration patterns, consideration of the physiological activity of both phytoplankton and microheterotrophs would undoubtedly explain a more significant fraction of the DFAA variation.This work is a contribution of GREPMA (Groupe Régional d'Etudes Pélagiques en Manche-Atlantique)     

Free protein amino acids of some Mediterranean Siphonales

Fifteen free protein amino acids have been quantitatively determined in nine green algae belongin to the order Siphonales. In all the species examined, aspartic acid, glutamic acid, alanine, glycine and serine dominate. Wide differences of the relative amounts of these amino acids in the various regardless of the genus were observed.     

Unnatural amino acids as probes of protein structure and function

Nonsense suppression methodology, for incorporating unnatural amino acids into proteins, has enabled a wide range of studies into protein structure and function using both in vitro and in vivo translation systems. Although methodological challenges remain, scores of unnatural amino acids have been employed that include both subtle and dramatic variants of the natural set. A number of insights that would not have been possible using conventional site-directed mutagenesis have been gained.     

混酸法降解植物纤维素技术研究

以单酸正交试验结果为基础,对二酸混合法和三酸混合法降解植物纤维素的最佳工艺条件进行了探讨。二酸混合法的结果表明,酸的添加顺序严重影响纤维素向葡萄糖的转化。强酸与弱酸同时混用均使葡萄糖的转化率降低。但盐酸与乙酸的混用效果则因所选最佳条件的不同而不同,虽然硫酸与盐酸均为无机强酸,与乙酸混用时添加的顺序亦一样即先弱酸后强酸,但其结果差别甚大,前者使葡萄糖的转化率降低,后者则使葡萄糖的转化率由40.9%锰增到62.7%。三酸混合法的结果表明,在本研究所选用的四种酸中,无论是哪三种酸同时混用,均使葡萄糖的转化率降低;当按一定顺序添加时,其结果亦不如二酸混合法,结论：在用多种酸降解植物纤维素时,一定要按一定的顺序添加,最好用两种酸即可。     

The response of muscle protein synthesis to nutrient intake in postabsorptive rats: The role of insulin and amino acids

In 12 h fasted rats, rates of muscle protein synthesis were stimulated by refeeding for 1 h and by intragastric or intravenous infusion of an amino acid plus glucose mixture for 1 hr, but not by intravenous infusion of amino acids alone for 1 h. Intravenous injection of anti-insulin serum suppressed the response to feeding and to intragastric infusion, but not to intravenous infusion. It is concluded that the response of muscle protein synthesis to food intake is mediated by both insulin and amino acids acting in concert.     

Increasing dispensable amino acids in diets of kittens fed essential amino acids at or below their requirement increases the requirement for arginine

Summary Kittens fed diets containing 0.75 × the NRC (1986) essential amino acid requirement (EAArq) and 210 to 560g crude protein(CP)/kg diet exhibited, with increasing CP: 1) decreasing weight gain, 2) decreasing plasma arginine concentrations, 3) increasing urinary orotic acid excretion, 4) increasing plasma glutamic acid concentrations, and 5) plasma isoleucine concentrations at levels that suggest a marginal isoleucine deficiency. Kittens fed a control diet (CD) containing 1.5 × EAArq and 350 g CP/kg diet had maximal weight gains and no orotic aciduria. It was concluded that the decreased weight gain and adverse metabolic effects were caused by arginine deficiency and possibly glutamic acid toxicity induced by high dietary dispensable amino acids. Kittens fed the diets containing 1.0 × EAArq and 350 and 560 g CP/kg diet had depressed plasma arginine and elevated glutamic acid concentrations and orotic aciduria. These results indicate that 10 g arg/kg diet is not adequate at CP concentrations above 280 g/kg and the calculated requirement of arginine is (0.02 g arginine/g CP) × (Y g CP/kg diet) + (4.0 g arginine/kg diet) where Y is the dietary CP level.Abbreviations CD control diet - CP crude protein (g CP/kg diet = g nitrogen/kg diet × 6.25) - DAA dispensable amino acids - EAA essential amino acids - EAArq essential amino acid requirement     

Lipophilicity of amino acids

Summary The lipophilicity (or hydrophobicity) of amino acids is an important property relevant for protein folding and therefore of great interest in protein engineering. For peptides or peptidomimetics of potential therapeutic interest, lipophilicity is related to absorption and distribution, and thus indirectly relates to their bioactivity. A rationalization of peptide lipophilicity requires basic knowledge of the lipophilicity of the constituting amino acids. In the present contribution we will review methods to measure or calculate the lipophilicities of amino acids, including unusual amino acids, and we will make a comparison between various lipophilicity scales.     

Gas chromatographic determination of total amino acids and protein in sediments using the ninhydrin-CO2 reaction

A sensitive modification of the ninhydrin-CO₂ method involving the gas chromatographic determination of the total protein and amino acid content of sediment is described. The method gives a linear response over the amino acid concentration range 10^–5 M to 4 × 10^–2 M. It can be used for whole sediment, hydrolysates and interstitial water. The performance of the method is compared with the fluorescamine method for primary amines.     

Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

Sequence alignment is a common method for finding protein structurally conserved/similar regions. However, sequence alignment is often not accurate if sequence identities between to-be-aligned sequences are less than 30%. This is because that for these sequences, different residues may play similar structural roles and they are incorrectly aligned during the sequence alignment using substitution matrix consisting of 20 types of residues. Based on the similarity of physicochemical features, residues can be clustered into a few groups. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. As a result, the accuracy of sequence alignment might be improved if the residues are properly clustered. Here, by using a database of aligned protein structures (DAPS), a new clustering method based on the substitution scores is proposed for the grouping of residues, and substitution matrices of residues at different levels of simplification are constructed. The validity of the reduced alphabets is confirmed by relative entropy analysis. The reduced alphabets are applied to recognition of protein structurally conserved/similar regions by sequence alignment. The results indicate that the accuracy or efficiency of sequence alignment can be improved with the optimal reduced alphabet with N around 9.     

Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

Sequence alignment is a common method for finding protein structurally conserved/similar regions. However, sequence alignment is often not accurate if sequence identities between to-be-aligned sequences are less than 30%. This is because that for these sequences, different residues may play similar structural roles and they are incorrectly aligned during the sequence alignment using substitution matrix consisting of 20 types of residues. Based on the similarity of physicochemical features, residues can be clustered into a few groups. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. As a result, the accuracy of sequence alignment might be improved if the residues are properly clustered. Here, by using a database of aligned protein structures (DAPS), a new clustering method based on the substitution scores is proposed for the grouping of residues, and substitution matrices of residues at different levels of simplification are constructed. The validity of the reduced alphabets is confirmed by relative entropy analysis. The reduced alphabets are applied to recognition of protein structurally conserved/similar regions by sequence alignment. The results indicate that the accuracy or efficiency of sequence alignment can be improved with the optimal reduced alphabet with N around 9. Supported by the National Natural Science Foundation of China (Grant Nos. 90403120, 10474041 and 10021001) and the Nonlinear Project (973) of the NSM     

Analysis of carbohydrates and amino acids in vegetable waste waters by ion chromatography

High-performance anion exchange chromatography coupled with pulsed amperometric detection was used for the quantitative determination of total and free sugars in olive oil mill waste waters (OMWW). Automated amino acid ion chromatography was employed to analyse total and free amino acids in the same OMWW. Sugars were analysed in samples pre-purified by means of a three-step purification procedure involving: (i) methanol precipitation of OMWW; (ii) dialysis of the obtained solid and liquid fractions; and (iii) chromatographic purification on RP18 phase followed by Amberlite resin. The amino acids were determined directly in samples obtained from the first two steps performed for sugar analysis. The analysis carried out with the reported methodologies allowed the quantitative determination of total sugars and amino acids and the differentiation between their free and bound forms. The sugars determined were arabinose, fructose, galactose, glucose, rhamnose, xylose, galacturonic and glucuronic acids, and the amino acids were Asp, Glu, Thr, Ser, Pro, Gly, Ala, Val, Met, Ile, Leu, Tyr, Phe, Lys, His, Arg and Cys. Asn, Gin, and Trp were not detected. The technological, biotechnological and environmental advantages arising from this analytical methodology applied to OMWW are briefly discussed.     

Changes in brain temperature and free amino acids in normal and protein deprived suckling rats exposed to room temperature

Previous reports on early-induced protein-calorie malnutrition (PCM) in rats have indicated alterations in the concentration of free amino acids and of protein synthesis in the brain. Recently it was shown that early-induced protein deprivation (PD) retards the development of thermoregulation. This resulted in a failure to maintain a normal rectal temperature after short exposure to room temperature (+22°C) still at the age of 20–25 days corresponding to changes seen in normal rats at an age of 10–15 days. In the present study, 20-day old PD and normal rats where examined with regard to the effect of exposure to room temperature on brain temperature and on brain free amino acids. The results show a similar reduction in brain and rectal temperature of the PD rats occuring within 30 minutes after exposure to room temperature. The reduction was in the range of 5°C. PD rats kept in room temperature for 5 hours and then allowed to recover at 32.5°C showed a slow increase in brain and rectal temperature but normal temperatures were not reached even after 1 hour. The concentration of free amino acids in the brain was examined in rats kept for 1 hour at room temperature or at 32.5°C. In the PD rats kept at 32.5°C, free aspartate and glutamate were reduced whereas taurine, GABA and glycine were increased as compared to their corresponding control rats. As a result of the reduced brain temperature in PD rats exposed to room temperature there was a reduction in free asparagine. The lability of the pool of asparagine may be related to the low levels of aspartate and glutamate in PD rats. On the basis of the present findings it is recommended that temperature-sensitive parameters are examined in PCM rats at a normal body temperature.Special Issue dedicated to Prof. Holger Hydén     

Changes with aging in the levels of amino acids in rat CNS structural elements II. Taurine and small neutral amino acids

Taurine (Tau) and the small neutral amino acids glycine (Gly), serine (Ser), threonine (Thr), and alanine (Ala) were measured in 53 brain areas of 3- and 29-month-old male Fisher 344 rats. The ratio of highest to lowest level was 34 for Tau, 9.1 for Thr, 7.6 for Gly and Ser, and 6.5 for Ala. The heterogeneity was found in numerous areas; for example, Tau levels were more than 90 nmol/mg protein in 6 areas, and less than 20 nmol/mg protein in 10 areas. Similar heterogeneity was found with the other amino acids. The relative distribution of the small neutral amino acids showed several similarities; Tau distribution was different. With age, four amino acids decreased in 10–18 areas, and increased in only 1–3, while Thr increased in more areas than it decreased. The five amino acids of this paper, and the four of the previous paper, are among the amino acids at highest level in the brain; the sequence in their levels shows considerable regional heterogeneity.     

Effect of dissolved free amino acids (DFAA) on the biomass and production of microphytobenthic communities

Mixed microphytobenthos communities, manipulated in two different ways in the laboratory (semi-natural and sediment-stripped), were examined for their response to dissolved free amino acids (DFAA) and nitrate (NO₃⁻). The semi-natural manipulation involved only the removal of macrofauna; and the sediment-stripped community used microfauna and flora that were separated from natural sediment and re-established on clean sediment, that is, certain indigenous nutrient sources were removed. Using sediment collected on two different occasions, two sets of experiments were made (3 and 4 week), under different light conditions. The response by the communities to the added nitrogen was measured as biomass (Chl a) and primary production. The stimulus from the DFAA addition on microphytobenthos biomass and primary production was similar to or higher than that from NO₃⁻. A conclusively positive effect from the nitrogen additions could be measured only in the sediment-stripped community. Compared to the semi-natural community, the sediment-stripped community responded faster to the added DFAA. When light was limiting, biomass and production by the sediment-stripped community was enhanced by the N additions, in particular by the DFAA addition. Results suggest that an efficient recycling of nitrogen allows generally nitrogen-poor sandy sediments to sustain high microphytobenthos productivity, thereby retaining nitrogen within the system.     

Effects of branched-chain amino acids on plasma amino acids in amyotrophic lateral sclerosis

Summary Although the cause of amyotrophic lateral sclerosis (ALS) remains unknown, biological findings suggest that the excitatory amino acid glutamate contributes to the pathogenesis of ALS. In previous studies of ALS, the therapeutic effect of the branched-chain amino acids (BCAAs) leucine, valine and isoleucine has been evaluated. The present study aimed at investigating the acute effect of BCAAs on plasma glutamate levels in ALS patients. Following two oral doses of BCAAs, significantly increased plasma levels were seen for valine (500%), isoleucine (1,377%) and leucine (927%), however the plasma level of glutamate was not affected. The plasma level of several other amino acids (tryptophan, tyrosine, phenylalanine and methionine) were found decreased after oral BCAAs, which may indicate a diminution in the rate of degradation of muscle protein and/or an increase in tissue disposal of amino acids.     

Sugar amino acids in designing new molecules

Emulating the basic principles followed by Nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create ‘nature-like’ and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature’s molecular arsenal. This article describes some of our works on various sugar amino acids and many other related building blocks, like furan amino acids, pyrrole amino acids etc. used in wide-ranging peptidomimetic studies. Published in 2005.Based on the invited lecture presented at the XVII International Symposium on Glycoconjugates held in January 12–16, 2003 at Bangalore, India.     

The importance of bacterivorous protists in the decomposition of stream leaf litter

1. Allochthonous organic matter, in the form of senesced leaves, is a major source of carbon supporting detrital food webs. While studies have documented the role of bacteria and fungi in the decomposition of leaf litter, little information is available regarding the role of protists in the decomposition process. 2. We tested the hypothesis that the presence of stream‐dwelling bacterivorous protists leads to an increased rate of leaf decomposition through grazing pressure on bacteria. We isolated live protists from decomposing leaves collected in a stream in Northern Virginia, U.S.A. (Goose Creek) and established laboratory cultures of common bacterivorous protists. 3. Recently senesced leaves from the field were used in laboratory microcosm experiments to determine if the rate of litter decomposition differed between four treatments: bacteria only, bacteria + flagellates, bacteria + flagellates + ciliates, autoclaved stream water (control). We determined the dry weight of leaf remaining, bacterial abundance, flagellate abundance and ciliate abundance for each replicate on days 0, 7, 14, 30, 60 and 120. 4. The rate of leaf decomposition was significantly higher in treatments with protists than without and bacterial abundance declined in protist treatments compared with bacteria only treatment. Weight loss in the presence of flagellates was three to four times higher when protists were present compared with treatments with bacteria alone. These results provide experimental evidence that protists could play a significant role in the detrital processes of streams.     

Free amino acids and protein concentrations in reproductive tract fluids of the mare

Uterine tubal fluids (UTF) were collected daily over a 214-day period (March through August) from three mares. Individual UTF samples identified by day of estrous cycle for five complete cycles within this six-month span were analyzed for free amino acids and total protein. Biochemical comparisons were made to blood plasma by drawing samples daily from each mare. Free amino acids and total protein were determined also on follicular fluids collected from three different mares on days 5 and 6 of standing estrus.The free amino acid level of UTF was significantly greater than was the amino acid concentration in blood plasma or follicular fluid. The highest concentration of amino acids in UTF was on day 13. Cyclic trends were observed for the amino acids, histidine, methionine, half-cystine, serine, proline, glycine, alanine, isolecine, and leucine. Glycine and alanine were found in the highest concentrations in UTF, peaking on day 17 of the estrous cycle. Protein concentration in UTF was highest on day 13 and lowest on days 7 and 19. Protein values for diestrus (33.1 mg/ml) were significantly greater (p<0.05) than for estrus (28.0 mg/ml).