Nucleic acid content as a potential growth rate estimator of Antarctic krill; results from field-caught krill from the indian sector of the southern ocean

Nucleic acid contents of tissue were determined from field-caught Antarctic krill to determine whether they could be used as an alternative estimator of individual growth rates which can currently only be obtained by labour intensive on-board incubations. Krill from contrasting growth regimes from early and late summer exhibited differences in RNA-based indices. There was a significant correlation between the independently measured individual growth rates and the RNA : DNA ratio and also the RNA concentration of krill tissue, although the strength of the relationship was only modest. DNA concentration, on average, was relatively constant, irrespective of the growth rates. The moult stage did not appear to have a significant effect on the nucleic acid contents of tissue. Overall, the amount of both nucleic acids varied considerably between individuals. Nucleic acid-based indicators may provide information concerning the recent growth and nutritional status of krill and further experimentation under controlled conditions is warranted. They are, however, reasonably costly and time-consuming measurements.     

Pelagic-benthic coupling of nucleic acids in an abyssal location of the northeastern Atlantic Ocean.

Spatial and temporal changes in sedimentary nucleic acid concentrations in an abyssal locality of the northeastern Atlantic Ocean were investigated in relation to fluxes of nucleic acids produced in the photic layer. Sediment trap material, collected between 1996 and 1998 at depths of 1,000, 3,000, and 4,700 m, and sediment samples were analyzed for DNA and RNA content. Nucleic acid concentrations in the sediments were very high and displayed significant temporal changes, whereas mesoscale variability was low. DNA and RNA concentrations generally displayed opposite temporal patterns, which are likely to be dependent on the nature and characteristics of DNA and RNA molecules. Nucleic acid fluxes were high and displayed clear seasonal changes apparently coupled with seasonal pulses of primary production. However, while median values of DNA fluxes were relatively similar in all sediment traps, median values of RNA fluxes almost doubled from the 1,000- to the 4,700-m depth, suggesting differences in the metabolic activity of microbes associated with sinking particles. Significant relationships between DNA concentrations in the sediments and DNA fluxes and between RNA concentrations and RNA fluxes, indicating the presence of a clear pelagic-benthic coupling of particulate nucleic acids, were observed. The benthic system investigated was not steady state since we estimated that, from September 1996 to October 1998, nucleic acid concentration in the sediments decreased by about 165 mg of DNA m(-2). Vertical profiles revealed a significant decrease in DNA concentration with depth in the sediments, reaching an asymptotic value of about 5 microg g(-1). This DNA fraction constitutes a pool of potentially refractory DNA (accounting for 16 to 40% of the total DNA pool) that might be buried in the sediments.     

Pelagic-Benthic Coupling of Nucleic Acids in an Abyssal Location of the Northeastern Atlantic Ocean

Spatial and temporal changes in sedimentary nucleic acid concentrations in an abyssal locality of the northeastern Atlantic Ocean were investigated in relation to fluxes of nucleic acids produced in the photic layer. Sediment trap material, collected between 1996 and 1998 at depths of 1,000, 3,000, and 4,700 m, and sediment samples were analyzed for DNA and RNA content. Nucleic acid concentrations in the sediments were very high and displayed significant temporal changes, whereas mesoscale variability was low. DNA and RNA concentrations generally displayed opposite temporal patterns, which are likely to be dependent on the nature and characteristics of DNA and RNA molecules. Nucleic acid fluxes were high and displayed clear seasonal changes apparently coupled with seasonal pulses of primary production. However, while median values of DNA fluxes were relatively similar in all sediment traps, median values of RNA fluxes almost doubled from the 1,000- to the 4,700-m depth, suggesting differences in the metabolic activity of microbes associated with sinking particles. Significant relationships between DNA concentrations in the sediments and DNA fluxes and between RNA concentrations and RNA fluxes, indicating the presence of a clear pelagic-benthic coupling of particulate nucleic acids, were observed. The benthic system investigated was not steady state since we estimated that, from September 1996 to October 1998, nucleic acid concentration in the sediments decreased by about 165 mg of DNA m⁻². Vertical profiles revealed a significant decrease in DNA concentration with depth in the sediments, reaching an asymptotic value of about 5 μg g⁻¹. This DNA fraction constitutes a pool of potentially refractory DNA (accounting for 16 to 40% of the total DNA pool) that might be buried in the sediments.     

玻璃粉吸附核酸及其在植物核酸提取中应用的研究

为研究玻璃粉在植物核酸提取中的应用,比较了玻璃粉颗粒大小、离液盐种类及浓度、pH等条件对玻璃粉吸附核酸的影响,得出玻璃粉吸附核酸的各种最佳条件。结果表明,普通玻璃粉吸附核酸能力强于硅胶和硅藻土,玻璃粉颗粒的直径以83 μm为佳,pH 4.0时吸附效果达到最大。提取DNA时,NaCl浓度应大于3 mol/L,而提取RNA时,异硫氰酸胍大于2 mol/L就能取得很好的效果,此外,在玻璃粉吸附RNA前,需要加入50%以上的无水乙醇才能更好地吸附。利用玻璃粉制作简易纯化柱,可用于植物组织核酸提取纯化,所提取的核酸纯度高、完整性好,可用于酶切、杂交和PCR等实验。与传统方法相比,采用玻璃粉简易离心柱提取植物核酸,效果好、环保、快速、经济。     

An RNA:DNA-based growth model for young-of-the-year winter flounder Pseudopleuronectes americanus (Walbaum)

A laboratory calibration experiment was conducted to determine the relationship between nucleic acid-based variables and growth rate in young-of-the-year winter flounder Pseudopleuronectes americanus . Three temperatures and three feeding levels were used to produce a variety of growth rates. Nucleic acid analyses were conducted on white muscle tissue using an ultraviolet absorption assay. RNA concentration (μg mg⁻¹ wet tissue mass) and the ratio of RNA:DNA ( R _RD) were positively correlated with a mass-based instantaneous growth coefficient ( G _M) ( r = 0·42 and 0·72, respectively). Fifty-one per cent of the variability in growth rate was explained by the simple linear regression G _M=−0·02615 + 0·00848 R _RD ( P < 0·001). This model can be used to estimate recent growth rates for early juvenile winter flounder (27–52 mm standard length) at temperatures ranging from 11 to 24° C.     

Biochemistry of the autolytic processes in Antarctic krill post mortem. Autoproteolysis.

1. Autoproteolysis post mortem was examined at 0 degree C by following the changes in the major classes of krill (Euphausia superba and Euphausia crystallorophias) proteins and by liberation of peptides and free amino acids, and was based on experiments conducted on board expedition vessels in the Antarctic. 2. Primarily salt-soluble proteins were broken down during the first week of incubation, whereas water-soluble and insoluble proteins were degraded to a much smaller extent. The enzymes responsible for the hydrolysis presumably originate primarily from the digestive apparatus of the krill. 3. In general, the individual amino acids were released at rates corresponding to their relative occurrence in the bulk protein of the krill. Alanine was liberated in larger amounts than would be expected from the composition of the krill protein, and was evidently formed also by reactions other than proteolysis. Glutamic acid, and certain amino acids which presumably occur with high frequency adjacent to glumatic acid residues in the krill protein, were liberated only to a limited extent, and accumulated in smaller peptides. 4. During proteolysis, arginine seemed to be converted to some degree into ornithine, and on prolonged incubation conversion of arginine and lysine into their corresponding decarboxylation products, agmatine and cadaverine, appeared to take place.     

Extraction of nucleic acids from lyophilized plant material

Four methods for extracting nucleic acids from lyophilized cotton (Gossypium hirsutum L. cv. Stoneville 62) leaves and roots were compared. They were based on the use of: (I) HC10₄; (II) KOH; (III) a mixture of 90% phenol, Tris (hydroxymethyl) aminomethane buffer, and sodium lauryl sulfate; and (IV) NaCl. (I) extracted large amounts of RNA but little DNA and extracted much carbohydrate and protein contaminants. (II) gave a good yield of both RNA and DNA but extracted such large amounts of contaminating material that purification of RNA on an anion exchange column was necessary. (III) extracted only part of the RNA and practically no DNA, but extracted contaminating materials. (IV) resulted in high yields of both RNA and DNA when modified to omit preliminary acid extraction of impurities. The use of cold trichloroacetic acid instead of ethanol, to precipitate NaCl-extracted nucleic acids, separated the nucleic acids from most of the carbohydrate and acid-soluble phosphate contaminants and resulted in good agreement among results by ultraviolet absorbance, pentose tests, and phosphate analysis. This method also resulted in lower protein contents and better ultraviolet absorption spectra than the other methods tested. Nucleic acids were extracted from leaves of 14 other species of plants, in addition to cotton, by this modified NaCl procedure.     

The determination of nucleic acids in freshwater plankton and its ecological implications *

Nucleic acid concentrations show large variations between different planktonic species. RNA concentration is much higher in phytoplankton than in zooplankton. DNA varies to a considerable extent, being five to six times higher in copepods than in cladocerans. In Daphnia hyalina, nucleic acid contents are proportional to dry weight during the whole life cycle except in newborn Daphnia where DNA concentration is abnormally high. Seasonal variations affect, to a large extent, nucleic acid concentrations. These results rule out the possibility of using nucleic acids as indicators of biomass in mixed planktonic populations.     

Two Circular Single-stranded DNAs Associated with Banana Bunchy Top Virus

Nucleic acids extracted from partially purified banana bunchy top virus (BBTV) consisted of 20 Kb DNA, 0.9-1.1 Kb DNA and 0.3 Kb RNA. Partially purified BBTV preparations predigested with DNase and RNase before particle disruption and nucleic acid isolation yielded only the 0.9-1.1 Kb DNA, but no corresponding nucleic acid band was obtained in total nucleic acid isolated from healthy banana tissue. Analysis of two BBTV cDNA clones showed that clone 1 consisted of 287 nucleotides and clone 2 contained a 1.0 Kb DNA insert. Clone 1 is not part of clone 2. When two pairs of primers, each pair in opposite orientation were used to amplify BBTV DNA by PCR using the total DNA from diseased banana tissues or DNA encapsidated in BBTV particle as the template, a DNA product of 1.1 Kb was generated by both, results indicating that the BBTV DNAs are circular. Additional results suggested that BBTV contained at least two circular ssDNAs designated BBTV essDNA I (containing clone 1 nucleotide sequence) and BBTV, cssDNA II (containing clone 2 nucleotide sequence).     

Two Circular Single-stranded DNAs Associated with Banana Bunchy Top Virus

Nucleic acids extracted from partially purified banana bunchy top virus (BBTV) consisted of 20 Kb DNA, 0.9–1.1 Kb DNA and 0.3 Kb RNA. Partially purified BBTV preparations predigested with DNase and RNase before particle disruption and nucleic acid isolation yielded only the 0.9–1.1 Kb DNA, but no corresponding nucleic acid band was obtained in total nucleic acid isolated from healthy banana tissue. Analysis of two BBTV cDNA clones showed that clone 1 consisted of 287 nucleotides and clone 2 contained a 1.0 Kb DNA insert. Clone 1 is not part of clone 2. When two pairs of primers, each pair in opposite orientation were used to amplify BBTV DNA by PCR using the total DNA from diseased banana tissues or DNA encapsidated in BBTV particle as the template, a DNA product of 1.1 Kb was generated by both, results indicating that the BBTV DNAs are circular. Additional results suggested that BBTV contained at least two circular ssDNAs designated BBTV cssDNA I (containing clone 1 nucleotide sequence) and BBTV cssDNA II (containing clone 2 nucleotide sequence).     

Secondary structure of nucleic acids in the folded chromosome from E. coli.

The circular dichroism of membrane-free folded chromosomes from E. coli was measured and analyzed. The spectrum can be explained as a simple linear combination of the individual spectra of E. coli RNA, and E. Coli DNA in the B form. No contribution from A form or C form DNA was detected. There was evidently some real variation in the ratio of the two nucleic acids from preparation to preparation, but the average value was 24% RNA and 76% DNA. No significant light scattering was observed and the analyses indicated no contribution to the circular dichroism from scattering artifacts. Apparently, combining DNA, RNA, and protein into membrane-free folded chromosomes does not change the secondary structure of the DNA or RNA from that found for the free nucleic acid in the same solvent system.     

Detecting growth under environmental extremes: Spatial and temporal patterns in nucleic acid ratios in two Antarctic bivalves

Growth of Antarctic benthic organisms is very slow due to temperature and food availability, and subtle differences in growth rate may be difficult to detect. Nucleic acid ratios (RNA/DNA, RNA/protein or total RNA concentration) are measures of protein synthesis potential and may be used to assess short-term growth rate in a range of marine organisms. We quantified nucleic acid ratios in the scallop Adamussium colbecki and the clam Laternula elliptica at five locations in the Ross Sea, Antarctica. We were able to detect species-specific, habitat-specific, and seasonal differences in nucleic acid ratios and related these to associated differences in primary productivity. By using nucleic acid ratios, future studies could relatively easily obtain a measure of growth rate from a multitude of locations with contrasting habitat characteristics, food availability and temperature regimes around the Antarctic continent. This would yield a unique understanding of spatial and temporal patterns in bivalve growth in this extreme environment.     

Simple molecular engineering of glycol nucleic acid: Progression from self-pairing to cross-pairing with cDNA and RNA

The acyclic chiral nucleic acid analogue, Glycol Nucleic Acid (GNA), displayed exceptional structural simplicity and atom economy while forming self-paired duplexes, using canonical Watson–Crick base pairing. We disclose here that the replacement of phosphodiester linker in GNA with somewhat rigid and shorter carbamate linker in Glycol Carbamate Nucleic Acid (GCNA) backbone allows unprecedented stability to the antiparallel self-paired duplexes. The R-GCNA oligomers were further found to form cross-paired antiparallel duplexes with cDNA and RNA following Watson–Crick base pairing. The stability of cross-paired GCNA:DNA and GCNA:RNA duplexes was higher than the corresponding DNA:DNA and DNA:RNA duplexes. The chiral (R) and (S) precursors were easily accessible from naturally occurring l-serine.     

Extraction of nucleic acids from agarose gels

A rapid, simple and versatile method is described for the extraction from agarose gels of small plasmid molecules and DNA fragments generated by restriction endonucleases. The method may be used also for the extraction of RNA from agarose-urea gels. It is based on the partitioning of nucleic acid molecules into 1-butanol as their quaternary ammonium salts, leaving the neutral agarose in the aqueous phase. The nucleic acid is then recovered as the sodium salt by partition back into an aqueous phase. Nucleic acid samples were found to be unaffected by the treatment, as judged by their ability to be ligated, transformed, nick-translated, and used in an in vitro protein-synthesizing system.     

绿豆子叶衰老期间核酸代谢的变化

萌发绿豆的子叶自然衰老期间,核酸含量降低,RNA降低的幅度比DNA大。电泳分析结果表明,子叶衰老期间细胞核主带DNA明显降低;而迁移慢的卫星带DNA变化不大。在RNA各组分中,18S rRNA从衰老前期就开始降低;25S rRNA和4～5S小分子RNA到衰老后期才缓慢下降。DNase和RNase活性在子叶整个衰老期间都明显升高,是导致核酸含量下降的主要原因。~3H-核苷掺入试验表明,核酸的合成速率在子叶衰老前期有所上升,到衰老后期又降低。poly(A)~ -mRNA含量在子叶开始衰老时明显上升。     

Breeding antarctic krill in captivity

Antarctic krill were maintained in large aquaria at Port of Nagoya Aquarium, Japan, under controlled photoperiod and were fed on phytoplankton and enriched animal feed. Maturation and spawning were induced after the light?:?dark (L?:?D) cycle was increased from 8?:?16 or 12?:?12 to 24?:?0, or when the L?:?D cycle was held constant at 14?:?10. This study is one of the first studies that demonstrate initiation of maturation and spawning events of krill under controlled photoperiod. Out of three experimental batches of krill, a total of 28 spawning events were observed. The mean number of eggs per event was 1424 with a range between 139 and 3458. The mean hatching success per batch was 19.1%. The relation between photoperiod and maturity/spawning is discussed. Furthermore, hatching is compared to previous studies and the reason for the low success is discussed.     

乳杆菌对数生长期培养基滤液核酸组分分析

目的通过对乳杆菌对数生长期培养基滤液中核酸组分的分析,阐明乳杆菌DM9811对数生长期培养基滤液中核酸的性质。方法应用核酸的分离、纯化及电泳分析技术。结果乳杆菌对数生长期培养基滤液中核酸组分为RNA,其片段大小为100 bp左右。乳杆菌对数生长期培养基滤液中核酸组分为RNA,为对数期产生且呈时间依赖关系。结论核酸组分不仅仅是遗传信息的载体,还可能作为有效的信息分子。     

Ontogenetic changes in RNA,DNA and protein contents of Chinese loach,Paramisgurnus dabryanus (Dabry de Thiersant, 1872), larvae and juveniles

The changes in nucleic acid‐based indices and protein variables of Chinese loach, Paramisgurnus dabryanus, larvae and juveniles from hatching to 60 days after hatching (DAH) were conducted to assess its growth potential. The nucleic acid contents were analysed using a UV‐based method (n = 3, rearing temperature 24.4 ± 0.4°C, dissolve oxygen 7.1 ± 0.5 mg L^?1, pH 7.9 ± 0.4). Ribonucleic acid (RNA) concentration significantly decreased from 2 to 5 DAH, then increased rapidly until 10 DAH, declining slightly thereafter. Deoxyribonucleic acid (DNA) concentration increased 2–5 DAH, decreased until 9 DAH, slightly increased again around 26 DAH, and then declined to a relatively stable level. Both RNA‐DNA and protein‐DNA ratios showed a statistically obvious relationship with growth rates. A significantly positive relationship was found between RNA‐DNA ratio and growth rates during the early life stage of Chinese loach. According to the results, growth of Chinese loach is characterized by rapid hyperplasia from hatching through completion of the yolk‐sac stage followed by continued rapid hyperplasia combined with increasing hypertrophy after feeding commences. The stage preceding 17 DAH of Chinese loach P. dabryanus is presumed to be critical for its survival and growth at 24°C.