Field evaluation by RNA/DNA ratios on post-release nutritional status of released and wild Japanese flounder Paralichthys olivaceus juveniles

A large-scale juvenile Japanese flounder (Paralichthys olivaceus) release-recapture experiment was undertaken to find the optimal release season by evaluating the nutritional status of released fish at different seasons during which food abundance was significantly different. Forty thousand fish were released at depths of 1.5 m for early-release (May 29, 1997) and 2 m for late-release (July 2, 1997) (42.1±3.5 and 40.9±4.2 mm body length, respectively) in an experimental field, Wakasa Bay, the Sea of Japan. Samples were taken, after the releases, at Wada beach at intervals of 1, 2, 3, 6, 10, 16 and 30 days after release (DAR), including pre-surveys before each release. Released fish recaptured from the two different release groups totaled 764; 467 from the early-release group (ER) and 297 from the late-release group (LR). A total of 1956 wild flounder juveniles were simultaneously collected (1041 ER, 915 LR). ER fish were subject to higher food availability and were exposed to less pressure from predation by smaller wild juvenile flounder. RNA/DNA ratios in ER juveniles were significantly higher than those of LR fish during all samples. Especially, RNA/DNA ratios in ER juveniles were higher than in wild juveniles from 3 to 50 DAR. In the LR group, the nutritional status of juveniles was relatively low in shallower water. These findings corresponded well with feeding incidence examined by coworkers. Mass release of hatchery-reared juveniles apparently reduced RNA/DNA ratio of the wild juveniles right after releasing. The present study showed that earlier release of hatchery-reared juvenile Japanese flounder with higher RNA/DNA ratio could increase the possibilities of survival right after release in the nursery ground, and that RNA/DNA ratio appeared to be a good tool in evaluating nutritional status of released juveniles as well as wild juveniles in Japanese flounder.     

Evaluating the nutritional condition of individual whitefish (Coregonus spp.) larvae by the RNA/DNA ratio

Larvae of Coregonus spp. were reared in the laboratory under different temperature (4, 6 and 8°C) and feeding conditions ( ad libitum , limited, with starvation intervals). Their RNA/DNA ratios were determined with a highly sensitive fluorescence technique. After resorption of their yolk reserves (about 2 weeks after hatching), well fed larvae (RNA/DNA >2.5) could be significantly distinguished from larvae reared under limited food supply (RNA/DNA < 2.5), both at the 6 and 8°C levels. At 4°C, no differences due to the feeding regime were found. During a second series of experiments, larvae were affected by an intestinal disease, which was caused by the ingestion of unsuitable copepod plankton. This disease provoked high mortality, decreased growth and RNA/DNA ratios which were almost as low as in temporarily starved larvae from the first series. Coregonid larvae sampled in Lake Constance during spring 1990 showed RNA/DNA ratios which were unexpectedly low when judged on the basis of mean body length and average ambient temperature. It was obvious from macroscopic observations that some of these wild larvae were severely attacked by the intestinal disease. The low RNA/DNA ratios in field samples are, therefore, interpreted as a sublethal result of this disease.     

Changes in RNA,DNA, protein contents and growth of turbot Scophthalmus maximus larvae and juveniles

The growth potential of turbot Scophthalmus maximus larvae and juveniles was studied using nucleic acid‐based indices and protein variables. The experiment was carried out from 4 to 60 days post hatching (dph). A significant increase in instantaneous growth rate during metamorphosis and retarded growth rate during post‐metamorphic phase were observed. Ontogenetic patterns of DNA, RNA and protein all showed developmental stage‐specific traits. The RNA:DNA ratio decreased up to 12 dph, then increased rapidly till 19 dph and fluctuated until 35 dph followed by a decline to the end. The RNA:DNA ratio was positively correlated with growth rate of juveniles during the post‐metamorphic phase, whereas this ratio was not a sensitive indicator of growth during the pre‐metamorphic phase and metamorphosis. The protein:DNA ratio showed a similar tendency to the RNA:DNA ratio. Changes of DNA content and protein:DNA ratio revealed that growth of S. maximus performed mainly by hyperplasia from 4 to 12 dph and hypertrophy until 21 dph during the pre‐metamorphic larval phase. Growth was dominantly hypertrophical from the early‐ to mid‐metamorphosing phase and hyperplastic thereafter. The results show that the DNA content and protein:DNA ratio can evaluate growth rates of larval and juvenile S. maximus on a cellular level.     

Morphological and biochemical approaches to assess the nutritional condition of the Argentine hake Merluccius hubbsi larvae from two different nursery areas

The Argentine hake, Merluccius hubbsi, is one of the most important fishing species in the Argentine Sea due to its great abundance and high-quality meat. The study of the nutritional condition is widely used to determine the physiological state of the fish larvae and to estimate their survival possibilities. The larval nutritional condition reflects the environmental conditions to which they have been exposed and represents a useful instrument to determine favourable nursery areas. It also provides tools for the comprehensive management of a population subjected to fishing exploitation. This study aimed to determine potential differences in the nutritional condition of M. hubbsi larvae from the two fishing stocks (Northern and Southern) of the species. The authors assessed the nutritional condition of larvae captured during the 2012 main reproductive peak in the nursery areas of each population. Two different methodologies were applied: a morphometrical approach, by recording five morphometric variables, and a biochemical technique, employing the RNA/DNA index (RD_s) and its derived index of growth performance. The morphometrical indexes did not show differences in the larval condition between both stocks. Nonetheless, the RD_s index did detect differences in the nutritional condition of larvae from different stocks. The RD_s index of larvae in pre-flexion and flexion stages showed significant differences between stocks, indicating that these stages are more susceptible to starvation. The results suggest that the biochemical indexes prove to be more sensitive than the morphometric indexes to detect slight differences in hake larvae nutritional condition. The scope and limitations of these techniques for the analysis of the nutritional condition of larvae are discussed.     

A review and assessment of the potential use of RNA:DNA ratios to assess the condition of entrained fish larvae

In rivers, lakes, and other aquatic systems throughout the world, intake pipes withdraw huge volumes of water for industrial purposes, including power plant cooling. During this process, large numbers of small-bodied, early life-stages of fish are pulled into pipes (i.e., entrained) and may be subjected to physical, thermal and chemical stress. As a result of such entrainment, these organisms can suffer direct or indirect mortality. However, given that the vast majority of larval fish are likely to die during early life due to natural processes, it is not obvious that entrainment-related mortality will have a strong influence on subsequent adult population sizes. The ability to evaluate if larval fish are dead on arrival, moribund, or in poor condition (i.e., likely to die through natural processes) at the time of entrainment could shed light on likely population-level impacts. To this end, we review the potential use of RNA:DNA ratios to index condition of entrained larval fish. Through a meta-analysis of published research studies, we demonstrate that RNA:DNA ratios of larval fish are responsive to starvation stress, with effect size increasing with duration of starvation. We relate these results to a surrogate measure of irreversible long-term negative impacts to fish populations, and demonstrate that the timescale over which RNA:DNA ratios respond to stress may not be long enough to reflect before-and-after entrainment stress. We also highlight the diverse factors contributing to variation of RNA:DNA ratios, including methodological, ontogenetic, and thermal influences. We believe that the need to account for these influences when comparing among RNA:DNA values limits the utility of broadly using RNA:DNA ratios to evaluate entrainment effects. However, the method shows promise as a quick and efficient means of determining fish condition and, used in proper context (e.g., specific to a given set of environmental conditions; in conjunction with other assessment techniques), may provide a powerful tool in assessing the effects of entrainment on fish populations. Assuming that researchers can account for sources of background variation, RNA:DNA analyses may be most useful for assessing the condition of fish larvae susceptible to entrainment (i.e., physically in the vicinity of the water intake) and/or evaluating whether fish larvae are likely to die from natural processes independent of entrainment.     

Nutritional condition, starvation status and growth of early juvenile Japanese sea bass (Lateolabrax japonicus) related to prey distribution and feeding in the nursery ground

The nutritional condition and protein growth rates of Japanese temperate bass larvae and juveniles were studied in relation to prey distribution and feeding habits in the nursery grounds in Chikugo estuary, Ariake Sea, Japan. Samples were collected from a wide spatial area covering the nursery grounds of the fish in March and April 2003. Food habits of the fish were analyzed by examining the gut contents. Fish condition was evaluated by using RNA/DNA ratio and other nucleic acid-based indices and protein growth rates. The nucleic acid contents in individually frozen larvae and juveniles were quantified by fluorometric method. Two distinguished feeding patterns, determined by the distribution of prey copepods, were identified along the nursery ground. The first pattern showed the dependency of the fish on the calanoid copepod Sinocalanus sinensis, which was the single dominant prey in low saline upper river areas and the second pattern involved a multi-species dietary habit mainly dominated by Acartia omorii, Oithona davisae and Paracalanus parvus. Values of RNA, DNA, total protein, growth rates and for all the nucleic acid-based indices were higher in upstream areas than in the downstream areas. The proportion of the starving fish was higher in the downstream areas than in the upstream areas. Condition of juvenile sea bass was not equal throughout the nursery grounds; fish in the upper river were in better condition than those in the lower estuary. We speculated that utilization of S. sinensis, which appears a suitable prey item and provide a better foraging environment in the upstream nursery ground, is one of the key factors for early survival and growth of Japanese temperate bass larvae and juveniles in the Chikugo estuary.     

RNA targeting by DNA binding drugs: Structural,conformational and energetic aspects of the binding of quinacrine and DAPI to A-form and H-form of poly(rC)·poly(rG)

A key step in the rational design of new RNA binding small molecules necessitates a complete elucidation of the molecular aspects of the binding of existing molecules to RNA structures. This work focuses towards the understanding of the interaction of a DNA intercalator, quinacrine and a minor groove binder 4′,6-diamidino-2-phenylindole (DAPI) with the right handed Watson–Crick base paired A-form and the left-handed Hoogsteen base paired H^L-form of poly(rC)·poly(rG) evaluated by multifaceted spectroscopic and viscometric techniques. The energetics of their interaction has also been elucidated by isothermal titration calorimetry. Results of this study converge to suggest that (i) quinacrine intercalates to both A-form and H^L-form of poly(rC)·poly(rG); (ii) DAPI shows both intercalative and groove-binding modes to the A-form of the RNA but binds by intercalative mode to the H^L-form. Isothermal calorimetric patterns of quinacrine binding to both the forms of RNA and of DAPI binding to the H^L-form are indicative of single binding while the binding of DAPI to the A-form reveals two kinds of binding. The binding of both the drugs to both conformations of RNA is exothermic; while the binding of quinacrine to both conformations and DAPI to the A-form (first site) is entropy driven, the binding of DAPI to the second site of A-form and H^L-conformation is enthalpy driven. Temperature dependence of the binding enthalpy revealed that the RNA–ligand interaction reactions are accompanied by small heat capacity changes that are nonetheless significant. We conclude that the binding affinity characteristics and energetics of interaction of these DNA binding molecules to the RNA conformations are significantly different and may serve as data for the development of effective structure selective RNA-based antiviral drugs.