Nuclear and cytoplasmic RNA in visual cortex neurons of adult rats following visual deprivation and photic stimulation

It has been shown by two-wavelength cytospectrophotometry of gallocyanin-chrome alum-stained sections that visual deprivation in adult rats kept in a complete darkness for 30 days resulted in an accumulation of cytoplasmic RNA by layer V neurons of the visual cerebral cortex and by the cells of the perineuronal neuroglia of this layer. The nuclear RNA content remained unchanged. Stimulation of intact rats with a flickering or constant light induced an increase in the cytoplasmic RNA in these neurons rather than in the nuclear RNA as well as in RNA in their glial satellite cells. Similar light stimulation of the deprived animals gave rise to a complete return of the neuronal RNA to normal with only a slight decrease in the deprivation-induced RNA accumulation by the neuroglial cells. Neither visual deprivation nor light stimulation affected the RNA content in the neurons and neuroglia of layer V of the motor cerebral cortex. Compartmentation of RNA metabolism within the neuronal-neuroglial unit is discussed.     

Protein SH-group concentration and RNA synthesis during the process of induction of proliferation in the stationary phase of cell culture growth]

The dynamics of intracellular protein SH-group (PSH) content was studied cytochemically in the course of stimulation of cell proliferation in stationary cultures of an established Chinese hamster cell line and of human diploid embryo fibroblasts. The results were compared with the pattern of RNA synthesis during the prereplicative period. In Chinese hamster cells immediately after medium changing in stationary cultures there is an augmentation of PSH content in parallel withe the increase in RNA synthesis rate. Later on, the rate of RNA synthesis and PSH content are seen decreasing followed by a new increase in the rate of RNA synthesis correlated with the second rise in PSH content. In stationary cultures of human diploid fibroblasts, there is also an increase in the rate of RNA synthesis and in the content of SH after medium changing, but the second wave of RNA synthesis and the second rise in PSH content are not pronounced. The variation in PSH content reflects the shift in the cell metabolism during the prereplicative period and is not attributed to changes in cell protein content.     

The RNA WikiProject: community annotation of RNA families

The online encyclopedia Wikipedia has become one of the most important online references in the world and has a substantial and growing scientific content. A search of Google with many RNA-related keywords identifies a Wikipedia article as the top hit. We believe that the RNA community has an important and timely opportunity to maximize the content and quality of RNA information in Wikipedia. To this end, we have formed the RNA WikiProject (http://en.wikipedia.org/wiki/Wikipedia:WikiProject_RNA) as part of the larger Molecular and Cellular Biology WikiProject. We have created over 600 new Wikipedia articles describing families of noncoding RNAs based on the Rfam database, and invite the community to update, edit, and correct these articles. The Rfam database now redistributes this Wikipedia content as the primary textual annotation of its RNA families. Users can, therefore, for the first time, directly edit the content of one of the major RNA databases. We believe that this Wikipedia/Rfam link acts as a functioning model for incorporating community annotation into molecular biology databases.     

CHANGES IN THE BASE COMPOSITION OF NUCLEAR RIBONUCLEIC ACID OF NEURONS DURING A SHORT PERIOD OF ENHANCED PROTEIN PRODUCTION

Nuclei from isolated nerve cells were sampled by microdissection. The content and composition of the nuclear RNA was studied and compared with that of the cytoplasmic RNA of Deiters' nerve cells of rabbits. Analyses were made of control nerve cells and of cells in which an enhanced RNA and protein production had been induced by chemical means, tricyano-amino-propene, for 60 minutes. The nuclear RNA content of the control nerve cells was 56 µµg, i.e. 3 per cent of the total RNA content of the nerve cell. The base ratios were: adenine 21.3, guanine 26.6, cytosine 30.8, uracil 21.3. Purine-pyrimidine analyses showed that the nuclear RNA differed significantly from the cytoplasmic RNA in having higher adenine and uracil values. The guanine and cytosine values were high, however, and the ratio G/C was 0.86 as compared with 1.16 for the cytoplasmic RNA. The composition of the nuclear RNA was interpreted as reflecting the extraordinarily strong development of the nucleolus in these neurons. During the 60 minutes of enhanced neuronal RNA production (+25 per cent) the guanine value increased and the uracil value decreased significantly in the nuclear RNA. In the cytoplasmic RNA the guanine value also increased although not so much as the nuclear guanine. The cytoplasmic cytosine value decreased. The result indicated that the production of the characteristic cytoplasmic RNA had been influenced by the change in the nuclear RNA     

CHANGES IN NUCLEAR RNA OF BRAIN INDUCED BY OLFACTION IN CATFISH

Abstract— —Studies were undertaken to correlate the changes in the synthesis of brain nuclear RNA during olfactory stimulation in saltwater catfish ( Galeichthys felis ). Catfish allowed to swim for 1 hr in sea water containing morpholine (10⁻⁴ M) showed an increase in brain nuclear RNA and a change in base ratios in contrast to controls in plain sea water. These changes in brain nuclear RNA were reversed within 24 hr to the levels of unstimulated controls when morpholine stimulated fish were transferred to fresh sea water.
In a split-brain preparation in an isolated catfish head, one naris was washed with morpholine in sea water (10⁻⁶ M), while the other naris was washed with plain sea water. The stimulated half of the brain, compared to the unstimulated half, showed the same changes in nuclear RNA as those noted in free swimming catfish. Brain cytoplasmic fractions did not exhibit any changes in RNA following olfactory stimulation. Amyl acetate, shrimp extract, and extracts from red fish skin as odorants also elicited changes in brain nuclear RNA. With each odorant there was an increase in amount of RNA and also a change in base ratio, where the base ratio changes were different for each odorant tested. With camphor as an odorant, there was an increase in brain nuclear RNA, while with menthol as an odorant, there was a decrease in brain nuclear RNA. In both instances the base ratio of the RNA did not change in contrast to the controls. These studies suggest that olfactory stimulants affect a change in content and character of the RNA in brain nuclei, whereas irritants to the olfactory epithelium change the content of brain nuclear RNA but do not alter the base ratio.     

Balbiani ring RNA content and half-life in nucleus and cytoplasm of Chironomus tentans salivary gland cells

The content of RNA with an origin in the Balbiani rings 1 and 2 (BR 1+2) has been determined in chromosomes, nuclear sap and cytoplasm of Chironomus tentans salivary gland cells. Together with information on rate and completeness of export this permits an estimation of half-life of this RNA in cytoplasm and its residence time in the nucleus. The quantities in the BR, nuclear sap, and cytoplasm are roughly related as 110200. The 75 S RNA in the nuclear sap with an origin in the BR 1+2 must to a high extent be a precursor to the cytoplasmic 75 S RNA in vivo. The half-life of the cytoplasmic component is about 20 h and the half-life (residence time) for BR 1+2 RNA in the nuclear sap around one hour. The presence of a large pool of BR RNA in the sap explains the previously observed delay in its cytoplasmic appearance in vivo.     

Effects of nitrogen and phosphorus starvation on nucleic acid and protein content of Heterocapsa sp.

Changes in the protein, RNA and DNA content related to nitrogen(N) and phosphorus (P) starvation were studied in the marinedinoflagellate Heterocapsa sp. grown in batch cultures. In bothcases of nutrient starvation, metabolic adaptations affectedprotein and RNA pools, while the DNA content per cell remainedapproximately constant. N starvation led to a parallel decreasein protein and RNA concentration which caused the protein/RNAratios to remain constant. A dramatic decrease in the RNA contentcharacterized the P-starved cultures, although protein synthesiscontinued. The ribosomal RNA content was lower than expectedgiven the continuation of protein synthesis. It is suggestedthat protein/RNA ratios could be used as an indicator of P starvation,while protein/chlorophyll ratios would characterize N starvation ¹Present address: University of Hawaii at Manoa Soest, BiologicalOceanography, 1000 Pope Road, Honolulu, HI 96822, USA     

Increase in the concentration of RNA in the blood erythrocytes of women in the ovulation period]

It was revealed that there was an increase (by an average of 58%) of the RNA concentration in the blood erythrocytes of women during ovulation. Measurement of the RNA content in erythrocytes can serve as an ovulation test.     

Polyadenylate sequences of human rhinovirus and poliovirus RNA and cordycepin sensitivity of virus replication.

The polyadenylate [poly(A)] content of the genome RNA of human rhinovirus type 14 (HRV-14) is nearly twice as large as that of the genome RNA of poliovirus type 2. The poly(A) content of viral RNA was determined to be the RNase-resistant fraction of 32P-labeled viral RNA extracted from purified virions. Polyacrylamide gel electrophoresis indicated that the poly(A) sequences of HRV-14 are more heterogenous and on an average larger than those of poliovirus RNA. On the basis of susceptibility to micrococcal polynucleotide phosphorylase the rhinovirus genome terminates in poly(A). Replication of both viruses is almost totally inhibited by cordycepin at 50 mug/ml. At lower concentrations, rhinovirus replication is more sensitive to cordycepin than poliovirus replication. Addition of cordycepin (75 mug/ml) to infected culture prior to or during viral RNA replication results in more or less complete inhibition of virus-specific RNA synthesis. The results do not indicate that cordycepin sensitivity of either virus is due to preferential inhibition of viral poly(A) synthesis by this antibiotic.     

Estimating the Growth Rate of Slowly Growing Marine Bacteria from RNA Content

In past studies of enteric bacteria such as Escherichia coli, various measures of cellular RNA content have been shown to be strongly correlated with growth rate. We examined this correlation for four marine bacterial isolates. Isolates were grown in chemostats at four or five dilution rates, yielding growth rates that spanned the range typically determined for marine bacterial communities in nature (μ = 0.01 to 0.25 h^-1). All measures of RNA content (RNA cell^-1, RNA:biovolume ratio, RNA:DNA ratio, RNA:DNA:biovolume ratio) were significantly different among isolates. Normalizing RNA content to cell volume substantially reduced, but did not eliminate, these differences. On average, the correlation between μ and the RNA:DNA ratio accounted for 94% of variance when isolates were considered individually. For data pooled across isolates (analogous to an average measurement for a community), the ratio of RNA:DNA μm^-3 (cell volume) accounted for nearly half of variance in μ (r² = 0.47). The maximum RNA:DNA ratio for each isolate was extrapolated from regressions. The regression of (RNA:DNA)/(RNA:DNA)_max on μ was highly significant (r² = 0.76 for data pooled across four isolates) and virtually identical for three of the four isolates, perhaps reflecting an underlying common relationship between RNA content and growth rate. The dissimilar isolate was the only one derived from sediment. Cellular RNA content is likely to be a useful predictor of growth rate for slowly growing marine bacteria but in practice may be most successful when applied at the level of individual species.     

A software tool-box for analysis of regulatory RNA elements

We describe an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format. It determines and rapidly scans the different regions of an RNA (including 5' UTR, CDS, 3' UTR in mRNA) and screens for specific RNA signals (in each of these regions, e.g. polyA-site, AU rich region etc. in 3' UTR). It runs a fast folding RNA routine to provide an overview of the RNA fold. Furthermore it analyzes structure content, fold energy and stem loops. In addition, consensus templates are used to determine whether there are any functional structures present for translational control (template: IRE), structured RNA (template: tRNA consensus) or catalytic RNA (template: trans-splicing RNA), giving indications as to how well the structures found match to these templates. The tool box has been implemented as a WWW server at http://wb2x01.biozentrum.uni-wuerzburg.de/.     

Ribonuclease Activity and Auxin Effects in the Lens Root

In Lens root tips, a direct proportionality between RNA and auxin levels and inverse proportionality between RNA content and RNase activity were found. IAA treatment of the Lens seedlings causes, in the root, both an increase of RNA and auxin content and a decrease of RNase activity. Addition of IAA to the excised roots produces an inhibition of both the decrease of the RNA levels and an inhibition of the increase of the RNase activity. The action of IAA on growth, related to the control of the RNA metabolism is discussed.     

The evolutionary transition from RNA to DNA in early cells

Summary The evolution of genetic material can be divided into at least three major phases: first, genomes of nucleic acid-like molecules; secondly, genomes of RNA; and finally, double-stranded DNA genomes such as those present in all contemporary cells. Using properties of nucleic acid molecules, we attempt to explain the evolutionary transition from RNA alone as a cellular informational macromolecule prior to the evolution of cell systems based on double-stranded DNA. The idea that ribonucleic acid-based cellular genomes preceded DNA is based on the following: (1) protein synthesis can occur in the absence of DNA but not of RNA; (2) RNA molecules have some catalytic properties; (3) the ubiquity of purine and pyridine nucleotide coenzymes as well as other similar ribonucleotide cofactors in metabolic pathways; and (4) the fact that the biosynthesis of deoxyribonucleotides always proceeds via the enzymatic reduction of ribonucleotides.The RNA prior to DNA hypothesis can be further developed by understanding the selective pressures that led to the biosynthesis of deoxyribose, thymine, and proofreading DNA polymerases. Taken together these observations suggest to us that DNA was selected as an informational molecule in cells to stabilize earlier RNA-protein replicating systems. These arguments include the facts that (1) the 2-deoxy-containing phosphodiester backbone is more stable in aqueous conditions and in the presence of transition metal ions (such as Zn²⁺) than its ribo-equivalents; (2) the absence of proofreading activity in RNA polymerases leads to a higher rate of mutation in RNA genomes relative to DNA; (3) information in RNA degrades because of the tendency of cytosine to deaminate to uracil and the lack of a correcting enzyme; and (4) UV irradiation produces a larger number of photochemical changes in RNA molecules relative to double-stranded DNA. The absence of atmospheric UV attenuation during the early Earth environment (Hadean and early Archean) would have imposed an intense selection pressure favoring duplex DNA over other genetic information storage systems.If RNA preceded DNA as a reservior of cellular genetic information, then an RNA-replicating oligopeptide must have been one of the earliest protoenzymes from which RNA polymerase presumably evolved. We conclude that RNA polymerases are among the oldest classes of enzymes.     

Embryonic development of 2 strains of mice in the early cleavage period

RNA metabolism at 1-, 2- and 8-celled stages was studied in C3H and C57Bl mice by means of detection of RNA content in individual embryos and microcolumnal chromatography of lysate of the embryos labelled with 3H-uridine. The increase of RNA content in the 8-celled embryos of the both strains is due to active synthesis of high and low molecular weight RNAs during this period. A comparison of 3H-uridine incorporation in RNA, and nucleotide fractions of 2-celled embryos has shown that the embryonic genome per se is activated earlier in C3H mice. The embryonic development and RNA changes in them are similar in the pure bred and hybrid embryos with common mothers. This serves as an additional evidence of the leading role of maternal factors in embryonic development during the first cleavage divisions.     

RNA editing

The term RNA editing describes those molecular processes in which the information content is altered in an RNA molecule. To date such changes have been observed in tRNA. rRNA and mRNA molecules of eukaryotes, but not prokaryotes. The demonstration of RNA editing in prokaryotes may only be a matter of time, considering the range of species in which the various RNA editing processes have been found. RNA editing occurs in the nucleus, as well as in mitochondria and plastids, which are thought to have evolved from prokaryotic-like endosymbionts. Most of the RNA editing processes, however, appear to be evolutionarily recent acquisitions that arose independently. The diversity of RNA editing mechanisms includes nucleoside modifications such as C to U and A to I deaminations, as well as non-templated nucleotide additions and insertions. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence.     

Nutritional condition of larval milkfish,Chanos chanos,occurring in the surf zone

In order to clarify the nutritional conditions of larval milkfish in the surf zone, the following parameters were examined: 1) DNA and RNA content and RNA/DNA ratio of fed and unfed larvae collected from the surf zone and reared in the laboratory; 2) survival rate of the unfed larvae; and 3) total length, otolith increment counts and RNA/DNA ratio of wild larvae collected daily from the surf zone. The DNA and RNA content of the unfed larvae decreased, but increased in fed larvae. The RNA/DNA ratio decreased in unfed larvae, whereas in the fed larvae it decreased for the first three days after capture and increased thereafter. These results indicated that the values of DNA and RNA content and RNA/DNA ratio could be used as an indicator of nutritional condition of milkfish larvae after 6 days of starvation. Although total length of the wild-larvae did not show serial changes, their otolith increment counts showed continuous increases, indicating that the larvae sojourned in the surf zone for several days. In the same period, RNA/DNA ratios of the wild larvae decreased continuously, the ratios of larvae with fewer otolith increment counts being relatively higher than those of larvae with greater increment counts. Based on these results, the milkfish larvae remaining in the surf zone were concluded as being under insufficient nutritional conditions.     

Dynamics of quantitative RNA changes in the Purkinje cells of the rat cerebellum in various functional states

UV cytophotometry was used to study over time the effect of vestibular stimulation on RNA content in Purkinje's cells of the rat cerebellum nodulus. The animals placed in narrow boxes were rotated horizontally (60 r.p.m.) for an hour. To evaluate partially the effects of stress and hypoxia, the content of RNA was examined in the immobilized animals placed in the same boxes without rotation. Rhythmic quantitative changes in RNA in the cytoplasm and nucleus of Purkinje cells were observed upon vestibular stimulation of cerebellum function. In the nucleolus, the changes in the content of RNA were less pronounced. The periodic quantitative changes in the content of RNA in the cytoplasm, nucleus and nucleolus of Purkinje cells were statistically significant in the majority of the animals, but weakly pronounced.