Identification of low-abundance differentially expressed transcripts using arrayed cDNA clones

Golby, Paul; Stephens, Sarah; Rast, Jonathan P.; Burke, Julian F.

doi:10.1016/s1096-4959(02)00146-x

Cited by 64 publications

(5 citation statements)

References 7 publications

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“…However, mean minimum ROS production did increase during experimentally induced hyperoxia, with this estimate likely to be conservative, especially in comparison with end-normoxia in the NAHN trial. Reperfusion with normoxic air after anoxia has been shown to cause physiological damage in Drosophila melanogaster [41] and many vertebrate species [42]. Therefore, it is likely that even during the NAN trial, ROS may have been produced in the end-normoxic phase, making the NAHN end-normoxia period similarly conservative.…”

Section: Discussionmentioning

confidence: 99%

“…The increase in minimum ROS production, and the changing variance in the system does suggest that ROS production and the system responsible for the removal thereof are significantly affected by experimentally induced hyperoxia. That experimental manipulation per se does not influence the variance is clear from the NAN trial, where the variance in changes in ROS production relative to normoxia remained low despite the different gas treatments (NAN SD range: [34][35][36][37][38][39][40][41][42][43]. By contrast, in the NAHN trial, variance of the relative ROS production was high-indeed the variation in this treatment was, on average, three to five times greater than that of the other treatments in the full set of experiments (NAHN SD range: 20-103).…”

Section: Discussionmentioning

confidence: 99%

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Reactive oxygen species production and discontinuous gas exchange in insects

et al. 2011

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While biochemical mechanisms are typically used by animals to reduce oxidative damage, insects are suspected to employ a higher organizational level, discontinuous gas exchange mechanism to do so. Using a combination of real-time, flow-through respirometry and live-cell fluorescence microscopy, we show that spiracular control associated with the discontinuous gas exchange cycle (DGC) in Samia cynthia pupae is related to reactive oxygen species (ROS). Hyperoxia fails to increase mean ROS production, although minima are elevated above normoxic levels. Furthermore, a negative relationship between mean _ V CO 2 and mean ROS production indicates that higher ROS production is generally associated with lower _ V CO 2 . Our results, therefore, suggest a possible signalling role for ROS in DGC, rather than supporting the idea that DGC acts to reduce oxidative damage by regulating ROS production.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Reactive oxygen species production and discontinuous gas exchange in insects

et al. 2011

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“…When very large numbers of ESTs are needed, serial-subtractive hybridization is an effective, but technically demanding, method for removing duplicate clones [ 22 , 23 ]. An alternative is cherry-picking of unique clones identified by filter hybridization [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags

et al. 2010

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BackgroundLarge collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research.ResultsThe ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10-10) to the UniProt database.ConclusionNormalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.

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“…The passive defense strategy of C. reevesii may result in animals taking refuge in an adverse environment, such as hiding underwater to escape predators but without access to air to breathe. There turtles can experience hypoxia/anoxia stress which is associated with excessive ROS generation in animal tissues [26]. A high constitutive antioxidant capacity favors the maintenance of redox balance without an extra energy investment when animals face with environmental stress frequently.…”

Section: Discussionmentioning

confidence: 99%

“…1a). At the same time, the present study also assessed on antioxidant capacity because it links with long-term fitness and stress tolerance [25, 26]. In the passive strategy, the use of long-term hiding in the shell may promote high constitutive antioxidant capacity.…”

Section: Introductionmentioning

confidence: 99%

Positive or negative? The shell alters the relationship among behavioral defense strategy, energy metabolic levels and antioxidant capacity in freshwater turtles

et al. 2019

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Background The relationships among energy metabolic levels, behavioral and other physiological traits help to determine the trade-off of energy allocation between different traits and the evolution of life-history driven by natural selection. However, these relationships may be distinctive in selected animal taxa because of their unique traits. In the present study, the relationships among energy metabolic levels, behavioral defense strategies, and antioxidant capacity were explored in three freshwater turtle species with different shell morphologies, by assessing responses to attack, righting time, shell morphology, whole-organism metabolic rates, tissue metabolic enzyme activities and antioxidant levels. Results The Chinese three-keeled pond turtles, Chinemys reevesii , showed a passive defense strategy, relatively larger shells, a higher resting metabolic rate (RMR) and higher antioxidant levels compared to the snapping turtle, Chelydra serpentina, or the Chinese soft-shelled turtle, Pelodiscus sinensis. These latter two species both showed an active defense strategy, a higher factorial aerobic scope and better muscle anaerobic metabolic capacity but relatively smaller shells, lower RMR and antioxidant capacity . Conclusion Our results indicate a negative relationship between RMR and activity levels in behavioral defense strategies along small-big shell continuum among the three turtle species. We also found a positive relationship between antioxidant capacity and energy metabolism but a negative one between antioxidant capacity and activity levels in defense strategies. The present study indicated a role of turtle shell in forming unique relationship between energy metabolic levels and behaviors in freshwater turtle taxa and a possible trade-off between the maintenance of physiological homeostasis and activity levels in energy allocation. Electronic supplementary material The online version of this article (10.1186/s12983-019-0301-5) contains supplementary material, which is available to authorized users.

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Identification of low-abundance differentially expressed transcripts using arrayed cDNA clones

Cited by 64 publications

References 7 publications

Reactive oxygen species production and discontinuous gas exchange in insects

Reactive oxygen species production and discontinuous gas exchange in insects

An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags

Positive or negative? The shell alters the relationship among behavioral defense strategy, energy metabolic levels and antioxidant capacity in freshwater turtles

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