scholarly journals A new approach to δ15N compound-specific amino acid trophic position measurements: preparative high pressure liquid chromatography technique for purifying underivatized amino acids for stable isotope analysis

2014 ◽  
Vol 12 (12) ◽  
pp. 840-852 ◽  
Author(s):  
Taylor A. B. Broek ◽  
Matthew D. McCarthy
2021 ◽  
Author(s):  
Philip Riekenberg ◽  
Tijs Joling ◽  
Lonneke L. IJsseldijk ◽  
Andreas M. Waser ◽  
Marcel van der Meer ◽  
...  

AbstractTraditional bulk isotopic analysis is a pivotal tool for mapping consumer-resource interactions in food webs but has largely failed to adequately describe parasite-host relationships. Thus, parasite-host interactions remain largely understudied in food web frameworks despite these relationships increasing linkage density, connectance, and ecosystem biomass. Compound-specific stable isotopes from amino acids provides a promising novel approach that may aid in mapping parasitic interactions in food webs. However, to date it has not been applied to parasitic trophic interactions.Here we use a combination of traditional bulk stable isotope analyses and compound-specific isotopic analysis of the nitrogen in amino acids to examine resource use and trophic interactions of five parasites from three hosts from a marine coastal food web (Wadden Sea, European Atlantic). By comparing isotopic compositions of bulk and amino acid nitrogen, we aimed to characterize isotopic fractionation occurring between parasites and their hosts and to clarify the trophic position of the parasites.Our results showed that parasitic trophic interactions were more accurately identified when using compound-specific stable isotope analysis due to removal of underlying source isotopic variation for both parasites and hosts, and avoidance of the averaging of amino acid variability in bulk analyses through use of multiple trophic amino acids. The compound-specific method provided clear trophic discrimination factors in comparison to bulk isotope methods, however, those differences varied significantly among parasite species.Amino acid compound specific isotope analysis has widely been applied to examine trophic position within food webs, but our analyses suggest that the method is particularly useful for clarifying the feeding strategies for parasitic species. Baseline isotopic information provided by source amino acids allows clear identification of the fractionation occurring due to parasite metabolism by integrating underlying isotopic variations from the host tissues. However, like for bulk isotope analysis, the application of a universal trophic discrimination factor to parasite-host relationships remains inappropriate for compound-specific stable isotope analysis. Despite this limitation, compound-specific stable isotope analysis is and will continue to be a valuable tool to increase our understanding of parasitic interactions in marine food webs.


2020 ◽  
Vol 7 ◽  
Author(s):  
Stephane Martinez ◽  
Maya Lalzar ◽  
Eli Shemesh ◽  
Shai Einbinder ◽  
Beverly Goodman Tchernov ◽  
...  

Amino acids compound-specific nitrogen stable isotope analysis (AA-CSIA) is an emerging tool in ecology for understanding trophic system dynamics. While it has been successfully used for several independent studies across a range of environments and study locations, researchers have encountered calculation issues for determining trophic position values. Most studies introduce modifications to the constants of trophic position equation calculations, but then fail to account for the equation variations when comparing across separate research studies. The broad acceptance of this approach is anchored in an underlying presumption that no addition of the exogenous nitrogen atom occurs in the different methods; and therefore, such variations should not affect the outcome. In this paper, we evaluate the use of the EZfaast amino acid derivatization kit (chloroformate) and compare it to the isotopic results of two other derivatization methods. We highlight new considerations for working with AA-CSIA that might account for some of the variations in the results and lead researchers to modify constants in the equation. This study concludes that developing unique constants per derivatization method is required to have more accurate cross-study comparisons of trophic positions.


Author(s):  
Stephane Martinez ◽  
Maya Lalzer ◽  
Eli Shemesh ◽  
Shai Einbinder ◽  
Beverly Goodman Tchernov ◽  
...  

AbstractAmino acids compound-specific nitrogen stable isotope (AA-CSIA) is an emerging tool in ecology for understanding trophic system dynamics. While it has been successfully used for several independent studies across a range of environments and study locations, researchers have encountered calculation issues for determining trophic position values. Most studies introduce modifications to the constants of trophic position equation calculations, but then fail to account for the equation variations when comparing the results of separate research studies. The acceptance of this approach is related to the underlying presumption that no addition of the exogenous nitrogen atom occurs in the different methods and, therefore, such variations should not affect the outcome. In this paper, we evaluate the use of the EZfaast amino acid derivatization kit (chloroformate) and compare it to the isotopic results of two other derivatization methods. We highlight new considerations for working with AA-CSIA that might account for some of the variations in the results and lead researchers to modify constants in the equation. This likely requires developing the unique constants per derivatization method in order to be able to compare the trophic position results across different studies.


2019 ◽  
Author(s):  
Rasmus Swalethorp ◽  
Lihini Aluwihare ◽  
Andrew R. Thompson ◽  
Mark D. Ohman ◽  
Michael R. Landry

AbstractCompound specific isotopic analysis of amino acids (CSIA-AA) is increasingly used in ecological and biogeochemical studies tracking the origin and fate of nitrogen (N). Its advantages include the potential for resolving finer-scale trophic dynamics than possible with standard bulk SIA and for reconstructing historical changes in the food webs of consumers from analyses of specimens in preserved sample archives. For the latter, assessing the effects of chemical preservatives on δ15NAA has been inconclusive because the conventional CSIA approach for derivatized AAs by gas chromatography – combustion – isotope ratio mass spectrometry (GC-C-IRMS) has analytical errors (0.4 - 1.0 ‰) in the range expected from chemical preservation. Here, we show improved analytical precision (0.15 ± 0.08 ‰) for 11 underivatized AA standards analyzed by high pressure liquid chromatography followed by offline elemental analysis – IRMS (HPLC/EA-IRMS), an approach originally developed by Broek and McCarthy (2014). Using this method, we report the first high-precision tests of preservation effects on δ15NAA in Northern Anchovy (Engraulis mordax) kept 1½-year in ethanol and up to 27-years in formaldehyde. We found minimal methodological induced fractionation for 8 AAs, and preservation effects on δ15N were similar regardless of duration and preservative used. Although some of the AAs differed significantly from frozen control samples (average +1.0 ± 0.8 ‰), changes in δ15N in the source AA Phenylalanine and trophic position estimates were statistically insignificant. Our results are encouraging for resolving fine-scale natural variability using HPLC/EA-IRMS on chemically preserved specimens and for ultimately reconstructing biogeochemical records and trophic dynamics over long time scales.


2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro

Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins specifically located in the cytoplasm, and two more in secreted proteins. Our results support the hypothesis that the characterization of Avoided Motifs in particular contexts can provide us with information about functional motifs, pointing to a new approach in the use of molecular sequences for the discovery of protein function.


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