Effect of river regulation on the life-history patterns of Barbus sclateri in the Segura river basin (south-east Spain)

The age structure, growth and reproduction of Barbus sclateri in a non-regulated section of the Segura River were similar to previously studied populations of undisturbed areas. Differences in the duration of the growth period or the reproductive cycle are considered evidence of the plasticity of the species as it adapts to different latitudes and local habitat characteristics. However, this population differed from one in a section with artificial water flow regulation. The non-regulated river population had a greater number of age groups, displayed a regular condition cycle, reached maturity earlier at lower ages and lengths and showed greater fecundity than the regulated river population. The mean lengths at age were longer in the regulated river population, possibly owing to the longer river section studied and/or to selective mortality of smaller specimens within a particular age group from the high water velocity when sluices are opened.     

Growth of North Alboran Sea sardine larvae estimated by otolith microstructure, nucleic acids and protein content

Wet mass and DNA, RNA and protein content increased significantly with standard length ( L _S) of sardine Sardina pilchardus larvae, collected in January 1995, in the Bay of Málaga, North Alboran Sea. L _S, wet mass and DNA, RNA and protein content were closely related allometrically to otolith radius ( R ). Larval daily length increments decreased but DNA, protein and wet mass daily increments increased with larval age. Daily length increments showed a negative and poor relationship with long-term otolith growth. In contrast, DNA, protein and wet mass daily increments were positively correlated. Differences between observed and back-calculated otolith radius-at-age indicated that larvae with slow otolith growth were under represented in older age groups, suggesting the existence of growth-selective mortality. Recent otolith growth, estimated from the mean widths of the last six increments, increased with age and R . Individual RNA: DNA and protein: DNA ratios were correlated significantly, although weakly, with L _S and larval growth.     

Studies on the retention of plasmid DNA and Escherichia coli nucleic acids by hydrophobic interaction chromatography

This work presents studies on the interactions of supercoiled plasmid DNA and Escherichia coli genomic DNA (gDNA) and RNA, with an hydrophobic interaction chromatography (HIC) gel, obtained by derivatisation of Sepharose CL-6B with 1,4-butanediol diglycidyl ether. Nucleic acids purified from E. coli were injected separately in the above HIC column and eluted with 1.5 M (NH₄)₂SO₄ in the buffer. The column was able to separate single-stranded from double-stranded nucleic acids. RNA and denatured gDNA were retarded in a different way due to the interactions of the exposed hydrophobic bases with the ligands. Supercoiled plasmid DNA, on the contrary, eluted in the flowthrough. This revised version was published online in July 2006 with corrections to the Cover Date.     

Changes in the metabolism of nucleic acids during the growth and senescence of tobacco callus

Changes in DNA and RNA metabolism, DNA composition and RNA species in callus of tobacco ( Nicotiana rustica L. cv. Gansu Yellow Flower) were investigated during the growth and senescence. DNA and RNA contents remained almost unchanged during the callus growth period, but started to decrease synchronously at the time that callus senescence was initiated. Synthesis of DNA and RNA, as measured by incorporation of [³H]-labelled precursor, increased during the growth period and did not decrease until late in senescence. The activities of DNase and RNase (pH 4.5) increased during the early senescence period in accordance with the decrease in the levels of DNA and RNA, but appeared to decrease during late senescence. These results suggest that the decrease in the levels of DNA and RNA in senescing tobacco callus may stem from the increase in the hydrolytic activities of DNase and RNase (pH 4.5) in the early stage of senescence, and that the slowdown of synthesis in the late senescence period may also be a cause. DNA and RNA electrophoresis showed that a low-molecular-weight satellite DNA band disappeared after the onset of senescence and that the nuclear main band DNA gradually decreased, whereas the high-molecular-weight satellite DNA seemed to undergo no significant changes during the senescence period tested. Of the RNA species, 4–5S RNA was far more susceptible to damage during senescence than 25S and 18S rRNA. This suggests different susceptibilities of different DNA and RNA components to damage during the senescence of tobacco callus or alternatively a highly sequenced degradation of DNA and RNA molecules.     

Synthesis of nucleic acids and localization of atrial natriuretic peptide in crayfish haemocytes

Three types of cells circulate in the haemolymph of the crayfish Astacus astacus, i.e., agranular haemocytes (HCs I), small-granule haemocytes (HCs II), and large-granule haemocytes (HCs III). Their proliferation, differentiation, and function remain poorly understood. Using light and electron microscopic autoradiography with [³H]-thymidine, we found that only HCs I are capable of DNA synthesis and mitosis whereas HCs II and HCs III are replicatively inactive. To verify whether HCs I are proliferating progenitor cells for granular HCs, we have analyzed autographs of the HC population 1, 2, 7, and 21 days after a single [3H]-thymidine administration. Contrary to our expectations, we have failed to find labeled HCs II and HCs III. These findings have raised doubts as to the capacity of HCs I to differentiate into two other types of HCs. With the use of ³H-uridine autoradiography, it was found that RNA synthesis was the most active in HCs I and 2 and 4 times lower in HCs II and HCs III, respectively. ANP-like immunoreactivity was revealed in large granules of the HCs III by electron microscopic immunocytochemistry. We assume that the presence of ANP in secretory granules extends the possible functions of crayfish HCs and suggests their participation in the regulation of the watersalt balance and immune response.     

Biomass Allocation of Scirpus mariqueter Along an Elevational Gradient in a Salt Marsh of the Yangtse River Estuary

cirpus mariqueter Tang et Zhang is a typical pioneer plant colonizing the bare beaches of the Yangtse River estuary. To explore the life history strategy of the species with reference to environmental physical stress, the biomass allocations to different plant components and some related morphological parameters were examined along an elevational gradient within a salt marsh. Authors found that S. mariqueter performed best at medium elevation within the marsh, with relatively high density of shoot and individual ramet dry mass. Biomass allocation to corm was the highest at low elevations, and the least at high elevations, suggesting that a conservative strategy was adopted by the species to cope with the harsh physical conditions at the low elevation. The investment in rhizome decreased from low to high elevations, while the proportion of inflorescence mass increased, indicating that during the life history, the species shifts from predominant asexual reproduction to predominant sexual reproduction. This may be favourable for the species to colonize larger area, and to spread and persist at a meta-population level. Correlation analyses showed that sexual reproduction was inversely related to growth and asexual reproduction. However, it is difficult to determine the relationship between asexual reproduction and growth possibly because of the varied function of the corms of the species in different life history stages.     

Changes in ribosome population and in nucleic acids during breaking of dormancy and development of apple flower buds

Changes in ribosome population, RNA species and DNA composition in flower buds of apples ( Malus pumila Mill. cvs Ralls and White winter pearmain) were investigated during breaking of dormancy and development. After bursting of flower buds, total ribosomes increased approximately 4-fold, and the polyribosomal fraction increased from 66% to 94% of total ribosomes. The newly synthesized ribosomes were identified by incorporation of radioactive precursor. The observed decrease in specific radioactivity of the monoribosomes is caused by the recruitment of monoribo-somes into polyribosomes after breaking of dormancy.
In both cultivars, the 25S and 18S rRNA peaks increased to a high level on April 8. The peaks of low molecular weight RNA were apparently increased after initial swelling of the flower buds. The DNA of flower buds was separated into three bands by electrophoresis. The median band is the main band of nuclear DNAs. The ahead band and the slow-moving band are satellite components of nuclear DNAs, and they obviously rose after initial swelling of the flower buds. On April 8, when the flower buds had opened, two other small DNA bands could be detected. These results suggest that the changes in level of different ribosome populations, RNA species and DNA composition are related to dormancy breaking development of apple flower buds.     

Fluorometric quantification of RNA and DNA in solutions containing both nucleic acids

A fluorescence-based method for quantitative determination of RNA and DNA in probes containing both nucleic acids has been developed. The total concentration of nucleic acids is determined using SYBR Green II dye under conditions providing independent binding of the fluorophore with DNA and RNA. The concentration of DNA is specifically measured using the Hoechst 33258 dye and the RNA concentration is calculated from these data. The procedure allows for accurate determination of DNA concentration in the range 10-1000 ng/ml in the presence of 200-fold excess of RNA and determination of RNA concentrations in the range 10-1000 ng/ml in the presence of large excess of DNA. An absence of the treatment of mixed samples with RNase-free DNase I provides rapid, reproducible, and accurate RNA quantification.     

Ultrastructural detection of nucleic acids within heat shock-induced perichromatin granules of HeLa cells by cytochemical and immunocytological methods

The perichromatin granules (PGs) are enigmatic structures of the cell nucleus. The major drawbacks for a biological study are their rare occurrence and their small size in normal conditions.As heat shock has been shown to increase their number, we applied a hyperthermal shock on HeLa cells to investigate the nucleic acid content of PGs by means of cytochemical and immunocytological approaches. These heat shock-induced PGs (hsiPGs) appeared as clusters organized in the form of honeycomb structures and were always associated with some blocks of condensed chromatin, such as the perinucleolar chromatin shell. A stalk connecting the hsiPG to the chromatin could be observed.For the detection of RNA, we applied an immunocytological method involving two anti-RNA antibodies and quantified the gold labelling obtained. The results clearly revealed that hsiPGs contained RNA.Regarding to the detection of DNA, we used three different methods followed by quantitative analyses. The results seemed to indicate that a small amount of DNA was present in hsiPGs.Together, these findings suggest that hsiPGs might be RNP structures associated with particular regions of DNA.     

Allocation of parental investment among individual offspring in the European beewolf Philanthus triangulum F. (Hymenoptera: Sphecidae)

Optimal allocation of parental resources is an important life history trait. However, it has been rarely investigated empirically. We tested aspects of optimal allocation theory in a digger wasp, the European beewolf. Investment allocation theory assumes (1) a trade‐off between investment per offspring and offspring number and (2) a convex relationship between investment per offspring and fitness returns. From mis relationship an optimum amount of investment per offspring can be derived and parents are predicted to provide each offspring with this optimum amount of investment. We used the number of bees in a brood cell as a measure of parental investment. Offspring fitness was quantified as both survival until emergence and success as adults. There is evidence for a trade‐off between current and future reproduction, suggesting that the first assumption is met. In contradiction to the second assumption, one mortality factor, parasitism, increased proportionally with the number of bees in a brood cell. However, overall mortality until emergence significantly decreased with the number of bees in a brood cell as assumed by the theory. The determination of the optimum amount of investment per offspring is complicated because the sexes possibly differ in their relationship between amount of investment and fitness. Individual males received considerably fewer bees (2.2 ± 0.8) than females (3.8 ± 0.5). Two independent estimates of the investment specific survival suggested that sons with two bees had the highest fitness returns per single bee and, consistent with the prediction, most sons were provisioned with two bees. For daughters, four bees is probably the optimum amount and most daughters were provisioned with this number. In both sexes the variation of investment per offspring was less than expected by a Poisson distribution with the same mean. These findings support the view that parental investment is allocated in a way that optimizes the trade‐off between offspring number and investment per offspring. However, variation contradicting the hypothesis still occurred. This might be explained either by adaptive variation in the amount of investment per offspring, constraints in the adjustment of the optimum amount of investment, or problems in measuring parental investment.     

Radical-generating coordination complexes as tools for rapid and effective fragmentation and fluorescent labeling of nucleic acids for microchip hybridization

DNA microchip technology is a rapid, high-throughput method for nucleic acid hybridization reactions. This technology requires random fragmentation and fluorescent labeling of target nucleic acids prior to hybridization. Radical-generating coordination complexes, such as 1,10-phenanthroline-Cu(II) (OP-Cu) and Fe(II)-EDTA (Fe-EDTA), have been commonly used as sequence nonspecific "chemical nucleases" to introduce single-strand breaks in nucleic acids. Here we describe a new method based on these radical-generating complexes for random fragmentation and labeling of both single- and double-stranded forms of RNA and DNA. Nucleic acids labeled with the OP-Cu and the Fe-EDTA protocols revealed high hybridization specificity in hybridization with DNA microchips containing oligonucleotide probes selected for identification of 16S rRNA sequences of the Bacillus group microorganisms.We also demonstrated cDNA- and cRNA-labeling and fragmentation with this method. Both the OP-Cu and Fe-EDTA fragmentation and labeling procedures are quick and inexpensive compared to other commonly used methods. A column-based version of the described method does not require centrifugation and therefore is promising for the automation of sample preparations in DNA microchip technology as well as in other nucleic acid hybridization studies.     

Fluorescence energy transfer monitored competitive equilibria of nucleic acids: Applications in thermodynamics and screening

Precise thermodynamic characterization of nucleic acid complex stability is required to understand a variety of biologically significant events as well as to exploit the specific recognition capabilities of nucleic acids in biotechnology, diagnostics, and therapeutics. The development of a database of nucleic acid thermodynamics with sufficient precision to foster further developments in these areas requires new and improved measurement techniques. The combination of a competitive equilibrium titration with fluorescence energy transfer based detection provides a method for precise measurement of differences in free energy values for nucleic acid duplexes that far exceeds in precision those accessible via conventional methods. The method can be applied to detect and to characterize any deviation in a nucleic acid that alters duplex stability. Such deviations include, but are not limited to, mismatches; single nucleotide polymorphisms (SNP); chemically modified nucleotide bases, sugars or phosphates; and conformational anomalies or folding motifs, such as, loops or hairpins. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 214–223, 2002     

Effects of copper deficiency on pollen fertility and nucleic acids in the durum wheat anther

Summary The effects of continuous copper deficiency and of temporary deficiencies initiated prior to (initial deficiency) or after (terminal deficiency) the end of tillering (a stage preceding the meiotic cycle) on pollen formation were investigated in durum wheat grown on a nutrient solution. The effects of the treatments on pollen viability (FCR test) and on the proline content of the pollen grains suggested that copper deficiency induced a nearly complete sterility of the pollen formed and inhibited all grain production. Temporary copper deficiencies significantly reduced the viability rate and the number of proline-rich pollen grains without affecting pollengrain production. Cytophotometric measurements showed that initial copper deficiency induced a significant increase in the proportion of polyploid microspore mother cells (MMCs), whereas terminal copper deficiency blocked endomitotic DNA syntheses. Protein metabolism was markedly altered by the treatments. The RNA content of the cytoplasm of tapetum cells was decreased by 34%–48%, depending on the treatment. The autoradiographic study showed that the stress caused by copper deficiency enhanced [³H]uridine incorporation into microspore cytoplasm RNA and also into the tapetum cells in the case of temporary deficiencies. The incidence of the treatments on the ploidy of the mother cells and on the disturbance of protein metabolism, particularly in tapetum cells, is discussed.     

Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues

Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13 years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen’s WaxFree method and our in-house phenol-chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion’s RecoverAll method recovered the most amplifiable RNA.     

Changes in the abundance of polyadenylated RNA during slime mould development measured using cloned molecular hybridization probes.

Total Dictyostelium discoideum messenger RNA prepared from cells at the eighth hour of development in suspension culture has been copied into DNA. This DNA was inserted into the plasmid PMB9 and used to transform Escherichia coli. The resulting “clone bank” was screened using an in situ hybridization technique in which replicate copies of a set of clones were hybridized with mRNA isolated from vegetative (non-developing) cells and from cells at the eighth hour of development. The mRNA was labelled in vitro so that the amount of hybridization to a given clone is a measure of the relative abundance of the mRNA complementary to the DNA in that clone. By comparing the amount of hybridization of the mRNA preparations to each clone, it has been possible to identify plasmids containing D. discoideum DNA whose complementary mRNA increases or decreases in abundance during development. These observations are direct proof of a change in mRNA concentration during D. discoideum development for individual high and medium abundance mRNA species. We can estimate from these results the proportion of such mRNA species whose concentration increases significantly during development and we find that only a small fraction show such a change.     

Hormonal control of tobacco protoplast nucleic acid metabolism during in vitro culture

Tobacco mesophyll protoplasts cultivated in vitro do not synthesize a measurable quantity of chloroplastic ribosomal RNA, but actively synthesize cytoplasmic ribosomal RNA, polyadenylated RNA, and proteins. These syntheses are essentially independent of the presence of hormones in the culture medium and are thus related to the ageing phenomenon induced by isolation from the plant and in-vitro culture. At all stages of culture and in all culture media, protoplasts incorporate low levels of thymidine into their DNA. However, the incorporation of considerable quantities of thymidine, indicative of the S phase, only takes place after 25–30 h and requires the presence of auxin and cytokinin.Abbreviations 6-BA 6-benzyladenine - 2,4-D 2,4 dichlorophenoxyacetic acid - DPC diethylpyrocarbonate - OD optical density; oligo-dT cellulose-oligothymidylic acid-cellulose - poly A⁺ RNA polyadenylated RNA - poly A^- RNA non-polyadenylated RNA - tRNA ribosomal RNA - SDS sodium dodecyl sulphate - TCA trichloroacetic acid - Tris buffer Tris (hydroxymethyl)aminomethane - tRNA transfer RNA     

Kinetin regulates plant growth and biochemical changes during maturation and senescence of leaves,flowers, and pods of <Emphasis Type="Italic">Cajanus cajan</Emphasis> L.

Aspects of plant growth such as height, branch number, leaf number, leaf area, pod area, 100-seed mass, etc., were correlated with biochemical changes such as contents of chlorophyll (Chl), proteins, DNA, and RNA, and protease activity during development and senescent phases in leaves, flowers, and pods of Cajanus cajan L. cv. UPAS-120 after treatments with kinetin (Kn). A significant increase was noticed in branch number, leaf number, leaf area, and seed mass while other growth processes registered a small increase after Kn application. Effectiveness of 5 μM Kn was also noticed in minimizing the loss of Chls, proteins, and nucleic acids as well as reducing the protease activity during maturity and senescence. Chl a/b ratio maintained a high value up to 30-d followed by a decline in leaves while flowers registered much lower ratio at 20-d-age. Pods were unique in having relatively lower ratio of Chl a/b in comparison to leaves.     

Structure,haemolymph titre,and regulatory effects of juvenile homone during ovarian maturation in Leucophaea maderae

Juvenile hormone (JH) synthesized and secreted in vitro by the corpora allata of mated adult Leucophaea maderae females was determined to be JH III (methyl-10,11-epoxy-3,7,11-trimethyl-2,6-dodecadienoate).The haemolymph titre of JH was determined during maturation of the terminal oöcytes in the first reproductive cycle of L. maderae. In virgin females, JH is not detectable in the haemolymph during the first eight days following adult emergence; however, by 10 days after emergence, trace quantities of JH are apparent. Mating stimuli induce a dramatic increase in the concentration of haemolymph JH, with a peak occurring approximately 12 days after mating; thereafter, the JH concentration declines until it has reached an undetectable level 19 days after mating, at the time of chorion deposition.During ovarian maturation, changes in the rates of synthesis of vitellogenin by the fat body and DNA by the ovary correlate closely with the haemolymph titre of JH. However, no such correlation exists between the JH titre and the extensive ovarian protein synthesis that occurs in L. maderae coincident with chorion formation.The effects of JH I and JH III on both vitellogenin synthesis and ovarain DNA synthesis are statistically similar.     

Adsorption and elution characteristics of nucleic acids on silica surfaces and their use in designing a miniaturized purification unit

We report nucleic acid (NA) adsorption isotherms and elution profiles for silica surfaces and use these to design a miniaturized NA purification unit based on solid-phase extraction with silica beads. The procedure is based on a pressure drop equation for flow through a packed bed and allows estimation of key design parameters such as channel dimensions, liquid flow rates, sample volume, and amount of silica needed. The usefulness of this design procedure is demonstrated by applying it to a column-based NA purification device for influenza detection for a case study of Madin-Darby canine kidney cells infected with influenza A virus.