Isotopic Discrimination in the Double-Crested Cormorant (Phalacrocorax auritus).
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ABSTRACT:
SUBMITTER: Craig EC
PROVIDER: S-EPMC4608772 | biostudies-other | 2015
REPOSITORIES: biostudies-other
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Project description:Stable isotope analysis has provided insights into the trophic ecology of a wide diversity of animals. Knowledge about isotopic incorporation rates and isotopic discrimination between the consumer and its diet for different tissue types is essential for interpreting stable isotope data, but these parameters remain understudied in many animal taxa and particularly in aquatic invertebrates. We performed a 292-day diet shift experiment on 92 individuals of the predatory mantis shrimp, Neogonodactylus bredini, to quantify carbon and nitrogen incorporation rates and isotope discrimination factors in muscle and hemolymph tissues. Average isotopic discrimination factors between mantis shrimp muscle and the new diet were 3.0 ± 0.6 ‰ and 0.9 ± 0.3 ‰ for carbon and nitrogen, respectively, which is contrary to what is seen in many other animals (e.g. C and N discrimination is generally 0-1 ‰ and 3-4 ‰, respectively). Surprisingly, the average residence time of nitrogen in hemolymph (28.9 ± 8.3 days) was over 8 times longer than that of carbon (3.4 ± 1.4 days). In muscle, the average residence times of carbon and nitrogen were of the same magnitude (89.3 ± 44.4 and 72.8 ± 18.8 days, respectively). We compared the mantis shrimps' incorporation rates, along with rates from four other invertebrate taxa from the literature, to those predicted by an allometric equation relating carbon incorporation rate to body mass that was developed for teleost fishes and sharks. The rate of carbon incorporation into muscle was consistent with rates predicted by this equation. Our findings provide new insight into isotopic discrimination factors and incorporation rates in invertebrates with the former showing a different trend than what is commonly observed in other animals.
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Project description:A decrease in the 13C/12C ratio of atmospheric CO2 has been documented by direct observations since 1978 and from ice core measurements since the industrial revolution. This decrease, known as the 13C-Suess effect, is driven primarily by the input of fossil fuel-derived CO2 but is also sensitive to land and ocean carbon cycling and uptake. Using updated records, we show that no plausible combination of sources and sinks of CO2 from fossil fuel, land, and oceans can explain the observed 13C-Suess effect unless an increase has occurred in the 13C/12C isotopic discrimination of land photosynthesis. A trend toward greater discrimination under higher CO2 levels is broadly consistent with tree ring studies over the past century, with field and chamber experiments, and with geological records of C3 plants at times of altered atmospheric CO2, but increasing discrimination has not previously been included in studies of long-term atmospheric 13C/12C measurements. We further show that the inferred discrimination increase of 0.014 ± 0.007‰ ppm-1 is largely explained by photorespiratory and mesophyll effects. This result implies that, at the global scale, land plants have regulated their stomatal conductance so as to allow the CO2 partial pressure within stomatal cavities and their intrinsic water use efficiency to increase in nearly constant proportion to the rise in atmospheric CO2 concentration.
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Project description:Stable isotope analysis (SIA) of highly migratory marine pelagic animals can improve understanding of their migratory patterns and trophic ecology. However, accurate interpretation of isotopic analyses relies on knowledge of isotope turnover rates and tissue-diet isotope discrimination factors. Laboratory-derived turnover rates and discrimination factors have been difficult to obtain due to the challenges of maintaining these species in captivity. We conducted a study to determine tissue- (white muscle and liver) and isotope- (nitrogen and carbon) specific turnover rates and trophic discrimination factors (TDFs) using archived tissues from captive Pacific bluefin tuna (PBFT), Thunnus orientalis, 1-2914 days after a diet shift in captivity. Half-life values for (15)N turnover in white muscle and liver were 167 and 86 days, and for (13)C were 255 and 162 days, respectively. TDFs for white muscle and liver were 1.9 and 1.1‰ for δ(15)N and 1.8 and 1.2‰ for δ(13)C, respectively. Our results demonstrate that turnover of (15)N and (13)C in bluefin tuna tissues is well described by a single compartment first-order kinetics model. We report variability in turnover rates between tissue types and their isotope dynamics, and hypothesize that metabolic processes play a large role in turnover of nitrogen and carbon in PBFT white muscle and liver tissues. (15)N in white muscle tissue showed the most predictable change with diet over time, suggesting that white muscle δ(15)N data may provide the most reliable inferences for diet and migration studies using stable isotopes in wild fish. These results allow more accurate interpretation of field data and dramatically improve our ability to use stable isotope data from wild tunas to better understand their migration patterns and trophic ecology.
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Project description:Nitrogen (N) isotopic discrimination (i.e. the difference in natural 15N abundance between the animal proteins and the diet; ?15N) is known to correlate with N use efficiency (NUE) and feed conversion efficiency (FCE) in ruminants. However, results from the literature are not always consistent across studies, likely due to isotopic discrimination pathways that may differ with the nature of diets. The objective of the present study was to assess at which level, from rumen to tissues, ?15N originates and becomes related to NUE and FCE in fattening yearling bulls when they are fed two contrasted diets. Twenty-four Charolais yearling bulls were randomly divided into two groups and fed during 8 months, from weaning to slaughter, either 1) a high starch diet based on corn silage supplying a balanced N to energy ratio at the rumen level (starch) or 2) a high fiber diet based on grass silage supplying an excess of rumen degradable N (fiber). All animals were slaughtered and samples of different digestive pools (ruminal, duodenal, ileal and fecal contents), animal tissues (duodenum, liver and muscle), blood and urine were collected for each animal. Ruminal content was further used to isolate liquid-associated bacteria (LAB), protozoa and free ammonia, while plasma proteins were obtained from blood. All samples along with feed were analyzed for their N isotopic composition. For both diets, the digestive contribution (i.e. the N isotopic discrimination occurring before absorption) to the ?15N observed in animal tissues accounted for 65 ± 11%, leaving only one third to the contribution of post-absorptive metabolism. Concerning the ?15N in digestive pools, the majority of these changes occurred in the rumen (av. ?15N = 2.12 ± 0.66‰), with only minor 15N enrichments thereafter (av. ?15N = 2.24 ± 0.41‰), highlighting the key role of the rumen on N isotopic discrimination. A strong, significant overall relationship (n = 24) between ?15N and FCE or NUE was found when using any post-absorptive metabolic pool (duodenum, liver, or muscle tissues, or plasma proteins; 0.52 < r < 0.73; P ? 0.01), probably as these pools reflect both digestive and post-absorptive metabolic phenomena. Fiber diet compared to starch diet had a lower feed efficiency and promoted higher (P ? 0.05) ?15N values across all post-absorptive metabolic pools and some digestive pools (ruminal, duodenal, and ileal contents). The within-diet relationship (n = 12) between ?15N and feed efficiency was not as strong and consistent as the overall relationship, with contrasted responses between the two diets for specific pools (diet x pool interaction; P ? 0.01). Our results highlight the contrasted use of N at the rumen level between the two experimental diets and suggests the need for different equations to predict FCE or NUE from ?15N according to the type of diet. In conclusion, rumen digestion and associated microbial activity can play an important role on N isotopic discrimination so rumen effect related to diet may interfere with the relationship between ?15N and feed efficiency in fattening yearling bulls.
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Project description:The use of biomarkers for feed conversion efficiency (FCE), such as Nitrogen isotopic discrimination (?15N), facilitates easier measurement and may be useful in breeding strategies. However, we need to better understand the relationship between FCE and ?15N, particularly the effects of differences in the composition of liveweight gain and rumen N metabolism. Alongside measurements of FCE and ?15N, we estimated changes in body composition and used dietary treatments with and without nitrates, and rumen metagenomics to explore these effects. Nitrate fed steers had reduced FCE and higher ?15N in plasma compared to steers offered non-nitrate containing diets. The negative relationship between FCE and ?15N was strengthened with the inclusion of fat depth change at the 3rd lumbar vertebrae, but not with average daily gain. We identified 1,700 microbial genes with a relative abundance >0.01% of which, 26 were associated with ?15N. These genes explained 69% of variation in ?15N and showed clustering in two distinct functional networks. However, there was no clear relationship between their relative abundances and ?15N, suggesting that rumen microbial genes contribute little to ?15N. Conversely, we show that changes in the composition of gain (fat accretion) provide additional strength to the relationship between FCE and ?15N.
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Project description:Stable isotopes of carbon and nitrogen characterize trophic relationships in predator-prey relationships, with clear differences between consumer and diet (discrimination factor Δ13C and Δ15N). However, parasite-host isotopic relationships remain unclear, with Δ13C and Δ15N remaining incompletely characterized, especially for helminths. In this study, we used stable isotopes to determine discrimination factors for 13 parasite-host pairings of helminths in coral reef fish. Differences in Δ15N values grouped according to parasite groups and habitat within the host with positive Δ15N values observed for trematodes and nematodes from the digestive tract and variable Δ15N values observed for cestodes and nematodes from the general cavity. Furthermore, Δ13C values showed more complex patterns with no effect of parasite group or habitat within host. A negative relationship was observed between Δ15N and host δ15N values among different host-parasite pairings as well as within 7 out of the 13 pairings, indicating that host metabolic processing affects host-parasite discrimination values. In contrast, no relationships were observed for Δ13C values. Our results indicate that parasite group, habitat within host, and host stable isotope value drive Δ15N of helminths in coral reef fish while their effect on Δ13C is more idiosyncratic. These results call for use of taxon- or species-specific and scaled framework for bulk stable isotopes in the trophic ecology of parasites.
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Project description:The interpretation of isotopic data in ecology requires knowledge about two factors: turnover rate and the trophic discrimination factor, which have not been well described in freshwater shrimps. We performed a 142-day diet shift experiment on 174 individuals of the omnivorous shrimp Macrobrachium borellii, measured their growth, and temporally serially sampled muscle and hepatopancreas tissue to quantify carbon and nitrogen incorporation rates and isotope discrimination factors. Shrimps were fed with artificial diets (δ13C = -26.1‰, δ15N= 2.1‰) for 45 days in attempt to standardize the shrimps' initial δ13C and δ15N values for subsequent experiments. Shrimps were then fed with another artificial diet (δ13C = -16.1‰, δ15N = 15.8‰) and the change in δ13C and δ15N was observed for a period of 97 days. The trophic discrimination factor (∆) for δ13C was significantly higher in hepatopancreas (0.7 ± 0.36‰) than in muscle (-0.1 ± 0.83‰); however, the opposite was the case for δ15N (1.7 ± 0.43‰ and 3.6 ± 0.42‰, respectively). In the hepatopancreas the mean residence time (τ) of 13C was 26.3 ± 4.3 days compared to a residence time of 16.6 ± 5.51 days for δ15N, whereas the τ in muscle was 75.8 ± 25 days for δ13C and 40 ± 25 days for δ15N. The rate of incorporation of carbon into muscle was higher than that predicted by allometric equations relating isotopic incorporation rate to body mass that was developed previously for invertebrates. Our results support ranges of traditional trophic discrimination factor values observed in muscles samples of different taxa (∆15N around 3‒3.5‰ and ∆13C around 0‒1‰), but our work provides evidence that these traditionally used values may vary in other tissues, as we found that in the hepatopancreas ∆15N is around 1.7‰.
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Project description:Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.
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Project description:The use of DNA microarrays to identify nucleotide variation is almost 20 years old. A variety of improvements in probe design and experimental conditions have brought this technology to the point that single-nucleotide differences can be efficiently detected in unmixed samples, although developing reliable methods for detection of mixed sequences (e.g. heterozygotes) remains challenging. Surprisingly, a comprehensive study of the probe design parameters and experimental conditions that optimize discrimination of single nucleotide polymorphisms (SNPs) has yet to be reported, so the limits of this technology remain uncertain. By targeting 24,549 SNPs that differ between two Saccharomyces cerevisiae strains, we studied the effect of SNPs on hybridization efficiency to DNA microarray probes of different lengths under different hybridization conditions. We found that the critical parameter for optimization of sequence discrimination is the relationship between probe melting temperature (Tm) and the temperature at which the hybridization reaction is performed. This relationship can be exploited through the design of microarrays containing probes of equal Tm by varying the length of probes. We demonstrate that using such a microarray we detect >90% homozygous SNPs and >80% heterozygous SNPs using the SNPScanner algorithm. The optimized design and experimental parameters determined in this study should guide DNA microarray designs for applications that require sequence discrimination such as mutation detection, genotyping of unmixed and mixed samples and allele-specific gene expression. Moreover, designing microarray probes with optimized sensitivity to mismatches should increase the accuracy of standard microarray applications such as copy number variation detection and gene expression analysis. Keyword(s): MutationDetection_CGH Comparison of polymorphic vs non-polymorphic genomes when hybridrized to short probe microarrays
2010-05-18 | E-GEOD-19319 | biostudies-arrayexpress
Project description:The use of DNA microarrays to identify nucleotide variation is almost 20 years old. A variety of improvements in probe design and experimental conditions have brought this technology to the point that single-nucleotide differences can be efficiently detected in unmixed samples, although developing reliable methods for detection of mixed sequences (e.g. heterozygotes) remains challenging. Surprisingly, a comprehensive study of the probe design parameters and experimental conditions that optimize discrimination of single nucleotide polymorphisms (SNPs) has yet to be reported, so the limits of this technology remain uncertain. By targeting 24,549 SNPs that differ between two Saccharomyces cerevisiae strains, we studied the effect of SNPs on hybridization efficiency to DNA microarray probes of different lengths under different hybridization conditions. We found that the critical parameter for optimization of sequence discrimination is the relationship between probe melting temperature (Tm) and the temperature at which the hybridization reaction is performed. This relationship can be exploited through the design of microarrays containing probes of equal Tm by varying the length of probes. We demonstrate that using such a microarray we detect >90% homozygous SNPs and >80% heterozygous SNPs using the SNPScanner algorithm. The optimized design and experimental parameters determined in this study should guide DNA microarray designs for applications that require sequence discrimination such as mutation detection, genotyping of unmixed and mixed samples and allele-specific gene expression. Moreover, designing microarray probes with optimized sensitivity to mismatches should increase the accuracy of standard microarray applications such as copy number variation detection and gene expression analysis. Keyword(s): MutationDetection_CGH
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