Transfer ribonucleic acid methylase activity in adult and fœtal rat liver

Foetal rat liver extracts were found to have higher tRNA methylase activities than corresponding extracts of adult liver. When the specific activities were expressed per mg of liver or per mg of protein, the foetal tRNA methylating enzymes were respectively 2.5 and 6 times higher than those of adult livers.The presence of an inhibitor in adult liver can be excluded, since the same recoveries of total tRNA methylase activity were obtained after partial purification of both adult and foetal liver extracts: yields were close to 100 per cent.The apparent Km's for the substrates in the methylating reactions were the same when tRNA methylases from either adult or foetal liver were used: values were 0.2 μM for Escherichia coli tRNA and 2.1 μM for S-adenosyl-l-methionine.After T₁-T₂ ribonuclease digestion of an in vitro methylated tRNA, similar methyl nucleotide patterns were observed in foetal and adult enzymatic extracts.It is concluded that the same tRNA methylase pool is present in adult and foetal liver. In addition, it is hypothesized that the different reaction rates exhibited by these enzymes might be due to the tRNA functional requirements rather than to the presence of a tRNA methylase inhibitor.     

Intragenomic Variation and Evolution of the Internal Transcribed Spacer of the rRNA Operon in Bacteria

Variation in the internal transcribed spacer (ITS) of the rRNA (rrn) operon is increasingly used to infer population-level diversity in bacterial communities. However, intragenomic ITS variation may skew diversity estimates that do not correct for multiple rrn operons within a genome. This study characterizes variation in ITS length, tRNA composition, and intragenomic nucleotide divergence across 155 Bacteria genomes. On average, these genomes encode 4.8 rrn operons (range: 2–15) and contain 2.4 unique ITS length variants (range: 1–12) and 2.8 unique sequence variants (range: 1–12). ITS variation stems primarily from differences in tRNA gene composition, with ITS regions containing tRNA-Ala + tRNA-Ile (48% of sequences), tRNA-Ala or tRNA-Ile (10%), tRNA-Glu (11%), other tRNAs (3%), or no tRNA genes (27%). Intragenomic divergence among paralogous ITS sequences grouped by tRNA composition ranges from 0% to 12.11% (mean: 0.94%). Low divergence values indicate extensive homogenization among ITS copies. In 78% of alignments, divergence is <1%, with 54% showing zero variation and 81% containing at least two identical sequences. ITS homogenization occurs over relatively long sequence tracts, frequently spanning the entire ITS, and is largely independent of the distance (basepairs) between operons. This study underscores the potential contribution of interoperon ITS variation to bacterial microdiversity studies, as well as unequivocally demonstrates the pervasiveness of concerted evolution in the rrn gene family. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Reviewing Editor: Dr. Margaret Riley     

Adipocyte size is associated with NAFLD independent of obesity,fat distribution,and PNPLA3 genotype

Objective: Adipocyte hypertrophy has been suggested to be causally linked with inflammation and systemic insulin resistance. The aim of the study was to determine whether increased adipocyte size is associated with increased liver fat content due to nonalcoholic fatty liver disease (NAFLD) in humans independent of obesity, fat distribution and genetic variation in the patatin‐like phospholipase domain‐containing 3 gene (PNPLA3; adiponutrin) at rs738409. Design and Methods: One hundred nineteen non‐diabetic subjects in a cross‐sectional study with a median age of 39 ( 26 ) years, mean ± SD BMI of 30.0 ± 5.7 kg m^?2 were studied. Abdominal subcutaneous (SC) adipocyte size, liver fat [proton magnetic resonance spectroscopy (¹H‐MRS)], intra‐abdominal (IA), and abdominal SC adipose tissue volumes [magnetic resonance imaging (MRI)] and the PNPLA3 genotype at rs738409 were determined. Univariate and multiple linear regression analysis were used to identify independent predictors of liver fat content. Results: In multiple linear regression analysis, age, gender, BMI, the IA/SC ratio, and PNPLA3 genotype explained 42% of variation in liver fat content. Addition of adipocyte size (P < 0.0001) to the model increased the percent of explanation to 53%. Thus, 21% of known variation in liver fat could be explained by adipocyte size alone. Conclusions: Increased adipocyte size highly significantly contributes to liver fat accumulation independent of other causes.     

Identification of a tRNA isopentenyltransferase gene from Arabidopsis thaliana

The tRNA of most organisms contain modified adenines called cytokinins. Situated next to the anticodon, they have been shown to influence translational fidelity and efficiency. The enzyme that synthesizes cytokinins on pre-tRNA, tRNA isopentenyltransferase (EC 2.5.1.8), has been studied in micro-organisms like Escherichia coli and Saccharomyces cerevisiae, and the corresponding genes have been cloned. We here report the first cloning and functional characterization of a homologous gene from a plant, Arabidopsis thaliana. Expression in S. cerevisiae showed that the gene can complement the anti-suppressor phenotype of a mutant that lacks MOD5, the intrinsic tRNA isopentenyltransferase gene. This was accompanied by the reintroduction of isopentenyladenosine in the tRNA. The Arabidopsis gene is constitutively expressed in seedling tissues.     

Origin and formation of 1,7-dimethylguanosine in tRNA chemical and enzymatic methylation

tRNA chemical methylation: 1. 1,7-Dimethylguanosine was found in in vivo methylated tRNA from liver and kidney of rat after exposure to a low dose of dimethylnitrosamine (4 mg/kg body weight). 2. At 4 h after dimethylnitrosamine administration, the 1,7-dimethylguanosine:7-methylguanine ratio (product ratio) for liver and kidney tRNA was 0.017 and 0.091, respectively. At 24 h after dimethylnitrosamine administration, the product ratio was lower in both hepatic and renal tRNA. 3. When dimethylnitrosamine was given in four separate daily injections, the product ratio in hepatic tRNA 4 h after the last dose was the same as for the same total dose given by a single injection, but in renal tRNA it was lower. No dialkyl compound was found in liver and kidney tRNA 24 h after the last multiple injection. tRNA enzymatic methylation: 1. Base analyses of Escherichia coli B tRNA methylated in vitro, by using S-adenosylmethionine as physiological methyl donor and enzyme preparations from liver and kidney of normal rat, indicated that 1,7-dimethylguanosine was also a product of enzymatic methylation. 2. The amount of 1,7-dimethylguanosine formed by kidney enzyme preparation was 3-times that produced by the liver extract. 3. A second type of enzymatic methylation assay where chemically methylated tRNA was used as substrate indicated that the 7-methylguanosine residues in the nucleic acid are not the substrate of the methylase activity forming the 1,7-dimethylguanosine moieties. Analogous data were obtained for the origin of 1,7-dimethylguanosine residues in tRNA chemical methylation by dimethyl sulphate.     

The stringent response to unacylated tRNA,energy- and temperature-downshift in Bacillus stearothermophilus

The response of the thermophile Bacillus stearothermophilus to inhibition of tRNA acylation, energy starvation and temperature downshift was characterized. We found that B. stearothermophilus, like other prokaryotic organisms, reacts with the so-called stringent response, which includes the accumulation of the unusual nucleotides guanosine 3′,5′ bis (dipphosphate) [ppGpp] and guanosine 3′-diphosphate, 5′-triphosphate [pppGpp] and concomitantly the reduction of RNA synthesis and growth rate. The amount of (p)ppGpp formed depended on the cause of the stringent response: when tRNA acylation was inhibited (p)ppGpp synthesis was much higher than after energy starvation or temperature downshift whereas RNA synthesis was totally blocked in each case.     

Stochastic density dependence in population size of a benthic clonal invertebrate: the regulating role of fission

The influence of environmental variation on the demography of clonal organisms has been poorly studied. I utilise a matrix model of the population dynamics of the intertidal zoanthid Palythoa caesia to examine how density dependence and temporal variation in demographic rates interact in regulating population size. The model produces realistic simulations of population size, with erratic fluctuations between soft lower and upper boundaries of approximately 55 and 90% cover. Cover never exceeds the maximum possible of 100%, and the population never goes to extinction. A sensitivity analysis indicates that the model’s behaviour is driven by density dependence in the fission of large colonies to produce intermediate sized colonies. Importantly, there is no density-dependent mortality in the model, and density dependence in recruitment, while present, is unimportant. Thus it appears that the main demographic processes which are considered to regulate population size in aclonal organisms may not be important for clonal species. Received: 18 August 1999 / Accepted: 29 October 1999     

Distribution of the modified nucleoside Q and its derivatives in animal and plant transfer RNA''s.

The modified nucleoside, 7-(4,5-cis-dihydroxy-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine, designated as Q, and its derivative, Q*, were found in tRNA's from various organisms, including several mammalian tissues, other animals such as starfish, lingula and hagfish, and wheat germ. Q isolated from rat liver tRNA was found to be identical with E. coli Q by mass spectrometry and thin-layer chromatography. Thus the rare modified nucleoside Q originally isolated from E. coli tRNA, is widely distributed in various organisms. Analysis of the mass spectrum of Q* suggested that it has a different side chain from Q.     

Relationships between environmental gradients and geographic variation in the intraspecific body size of three species of frogs (Anura)

The relationship between environmental gradients and patterns of geographic variation in body size has been a controversial topic for ectothermic organisms globally. To examine whether the patterns that generally hold in more temperate species also hold for tropical ones, we examined the intraspecific body size variation in three species of Neotropical frogs, Dendropsophus minutus, Hypsiboas faber and Physalaemus cuvieri, along different environmental gradients (e.g. temperature, precipitation and topography). We analysed four competing hypotheses: (i) the water availability hypothesis that predicts a negative relationship between body size and precipitation; (ii) the heat balance hypothesis that predicts a negative relationship between body size and temperature; (iii) the topography hypothesis that predicts a negative relationship between body size and altitude; and (iv) the mixed‐effect hypothesis that predicts that individuals occurring in wet and cold sites would be larger than individuals occurring in dry and warm sites. The spatial pattern of geographic variation in body size among populations of H. faber was associated with the mixed‐effect hypothesis. In localities with low precipitation seasonality and cold conditions, H. faber individuals were larger than in localities with high precipitation seasonality and warm conditions. Variation in the body size of D. minutus was the opposite of that predicted by the heat balance hypothesis. Individuals in localities with high temperatures were larger than in localities with low temperatures. On the other hand, variation in the body size of P. cuvieri was not associated with the variables used in this study. Our results suggest that intraspecific variation in anuran body size is more dependent on species‐specific response than on the region (i.e. temperate or tropical) where they occur.     

Size is not everything: a meta‐analysis of geographic variation in microscopic eukaryotes

Aim To analyse how important body size is for geographic variation in microscopic organisms in the marine environment and thereby determine the validity of the ‘everything is everywhere’ hypothesis. Location Marine environments, globally. Methods Studies on geographic variation in all marine eukaryotes smaller than 1 mm and all marine copepods were compiled from the literature and incorporated in multiple binomial regressions to analyse the effect of body size, lifestyle, environmental isolation and taxonomic affinity on the probability of different regions being reciprocally monophyletic. Sample size was also analysed, because a negative relationship between sample size and probability of being reciprocally monophyletic would indicate biases due to undersampling in the original studies. Separate analyses were performed for three potential types of barriers to gene flow for marine organisms (the water barrier of the middle of the oceans, the temperature barrier of the equator, and the land barrier of the continents). Results Environmental isolation was the only variable in the best‐fitting model for the probability of populations from each side of an ocean being reciprocally monophyletic. The estimated importance of body size was quite large and the lack of this variable in the best‐fitting model may be a power issue due to the small sample size (n= 40). Both environmental isolation and body size were important for the probability of monophyletic populations in different hemispheres. The analysis of isolation between different oceans did not produce clear results. The relationship between sample intensity and probability of being reciprocally monophyletic was positive for the isolation between different oceans and non‐existent for the two other analyses. Main conclusions The results showed that body size was an important factor governing the potential for geographic variation but not the only important factor by far. These results clearly weaken the ‘everything is everywhere’ hypothesis as they showed that microscopic organisms may have geographic variation, albeit to a lesser degree than larger organisms.     

Sequence Variation in the tRNA Genes of Human Mitochondrial DNA

Recent analyses have shown that nonsynonymous variation in human mitochondrial DNA (mtDNA) contains nonneutral variants, suggesting the presence of mildly deleterious mutations. Many of the disease-causing mutations in mtDNA occur in the genes encoding the tRNAs. Nucleotide sequence variation in these genes has not been studied in human populations, nor have the structural consequences of nucleotide substitutions in tRNA molecules been examined. We therefore determined the nucleotide sequences of the 22 tRNA genes in the mtDNA of 477 Finns and, also, obtained 435 European sequences from the MitoKor database. No differences in population polymorphism indices were found between the two data sets. We assessed selective constraints against various tRNA domains by comparing allele frequencies between these domains and the synonymous and nonsynonymous sites, respectively. All tRNA domains except the variable loop were more conserved than synonymous sites, and T stem and D stem were more conserved than the respective loops. We also analyzed the energetic consequences of the 96 polymorphisms recovered in the two data sets or in the Mitomap database. The minimum free energy (ΔG) was calculated using the free energy rules as implemented in mfold version 3.1. The ΔG’s were normally distributed among the 22 wild-type tRNA genes, whereas the 96 polymorphic tRNAs departed significantly from a normal distribution. The largest differences in ΔG between the wild-type and the polymorphic tRNAs in the Finnish population tended to be in the polymorphisms that were present at low frequencies. Allele frequency distributions and minimum free energy calculations both suggested that some polymorphisms in tRNA genes are nonneutral.Reviewing Editor: Dr. Rüdiger Cerff     

Separation of MET-tRNAf- and MET-tRNAm by Chromatography On Sepharose 4B Columns

Unfractionated rabbit liver tRNA, charged with [³H]methionine by use of rat liver enzymes, was separated into two [³H]methionine-containing fractions by column chromatography on Sepharose 4B. The two fractions were identified as Met-tRNA_m ^Met and Met-tRNA_f ^met by (a) their different ability to form a GTP- -dependent ternary complex with IF-MP, and (b) the absence of the first fraction after selective charging of the tRNA with E. coli amino acyl tRNA synthetase. The methionine residue was without noticeable influence on the separation.     

The effect of seed traits on geographic variation in body size and sexual size dimorphism of the seed‐feeding beetle Acanthoscelides macrophthalmus

Explaining large‐scale patterns of variation in body size has been considered a central question in ecology and evolutionary biology because several life‐history traits are directly linked to body size. For ectothermic organisms, little is known about what processes influence geographic variation in body size. Changes in body size and sexual size dimorphism (SSD) have been associated with environmental variables, particularly for Bruchinae insects, which feed exclusively on seeds during the larval stage. However, the effect of important seed traits on body size variation has rarely been investigated, and whether SSD varies substantially among populations within bruchine species is poorly known. Using the seed‐feeding beetle Acanthoscelides macrophthalmus infesting its host plant Leucaena leucocephala, we investigated whether specific seed traits (hardness, size, water content, carbon/nitrogen ratio, and phenolic content) were determinant in generating geographic variation in body size and SSD of A. macrophthalmus. We also examined the relationships between body size and SSD with latitude and altitude. The body size of both sexes combined was not related to latitude, altitude, and any of the physical and chemical seed traits. However, the female body size tended to vary more in size than the males, generating significant variation in SSD in relation to latitude and altitude. The females were the larger sex at higher latitudes and at lower altitudes, precisely where seed water content was greater. Therefore, our results suggest that water content was the most important seed trait, most severely affecting the females, promoting geographic variation in SSD of A. macrophthalmus.     

The absence of ribothymidine in specific eukaryotic transfer RNAs. I. Glycine and threonine tRNAs of wheat embryo

Ribothymidine, generally considered a universal nucleotide in tRNA, is completely absent in five specific wheat embryo tRNAs. These consist of two species of glycine tRNA and three species of threonine tRNA. These tRNAs, all extensively purified, are acceptable substrates for $\text{E. coli}$ - ribothymidine forming-uracil methylase, which produces one mole of ribothymidine per mole of tRNA. These five tRNAs account for about 90% of the wheat embryo tRNAs which are substrates for this methylase. Nucleotide sequence analysis of one of these tRNAs, tRNA^Gly_I, confirmed both the complete absence of ribothymidine at position 23 from the 3′end, and the presence of uridine at that site instead. In addition, it is shown that methylation with $\text{E. coli}$ uracil methylase quantitatively converts uridine at position 23 to ribothymidine, while no other uridine in the molecule is affected.Using $\text{E. coli}$ uracil methylase as an assay we have detected this class of ribothymidine lacking tRNA, in each case consisting of a few specific species, in other higher organisms, such as wheat seedling, fetal calf liver and beef liver, in addition to wheat embryo. We could not detect this class of tRNA in $\text{E. coli}$ or yeast tRNA.     

A comparison of tRNA populations of rat liver and skeletal muscle during aging

Total tRNA extracted from liver as well as from skeletal muscle of young, adult and old female albino rats showed quantitative variation with age. The amount of liver total tRNA was maximum in adult rats when compared to that in young and old ones, whose levels were almost the same. Transfer RNA from skeletal muscle showed a different pattern with age. It was maximum in young rats and showed a gradual decline with age. Transfer RNAs were aminoacylated using homologous synthetase preparations to study their qualitative variation during aging, which followed the trend of quantitative variation in both the tissues. Arginyl and glutamyl-tRNAs were fractionated from both the tissues at the three ages. Isoacceptor profile of glutamyl-tRNAs showed neither tissue specificity nor age-related change, whereas a definite change was found in the case of arginyl-tRNA isoacceptors in the two tissues during aging.     

Thorson's rule,life‐history evolution,and diversification of benthic octopuses (Cephalopoda: Octopodoidea)

Here, we evaluate the so‐called Thorson's rule, which posits that direct‐development and larger eggs are favored toward the poles in marine organisms and whose validity been the subject of considerable debate in the literature, combining an expanded phenotypic dataset encompassing 60 species of benthic octopuses with a new molecular phylogeny. Phylogenetic reconstruction shows two clades: clade 1 including species of the families Eledonidae, Megaleledonidae, Bathypolypodidae, and Enteroctopodidae, and clade 2 including species of Octopodidae. Egg size, development mode, and all environmental variables exhibited phylogenetic signal, partly due to differences between the two clades: whereas most species in clade 1 inhabit cold and deep waters, exhibit large eggs and hatchling with holobenthic development, species from clade 2 inhabit tropical‐temperate and shallow waters, evolved small eggs, and generally exhibit merobenthic development. Phylogenetic regressions show that egg size exhibits a conspicuous latitudinal cline, and that both egg size and development mode vary with water temperature. Additionally, analyses suggest that egg size is constrained by body size in lineages with holobenthic development. Taken together, results suggest that the variation in egg size and development mode across benthic octopuses is adaptive and associated with water temperature, supporting Thorson's rule in these organisms.     

Development and evaluation of a new device to effectively detach micro-organisms from food samples

Aims: To develop a new instrument of great versatility for recovering micro‐organisms from all types of food samples and to compare the effects with existing sample preparation methods. Methods and Results: To detach micro‐organisms from large‐size unbroken food samples such as apples, carrots, potatoes and tomatoes without preprocessing, the Spindle apparatus was newly developed. The Spindle was used to effectively detach micro‐organisms from large‐size samples. In a comparative study involving 51 food samples, treatment with the Spindle and Stomacher showed that recovery of total aerobic micro‐organisms (naturally occurring mesophilic microflora) and foodborne pathogens (from samples inoculated with Escherichia coli O157:H7, Salmonella Typhimurium and Listeria monocytogenes) for both methods was highly correlated (R² = 0·98). Furthermore, diluents treated by the Spindle contained much less food debris than those treated by stomaching. Conclusions: These results indicate that Spindle is a novel, effective alternative method for detaching micro‐organisms from food samples including four kinds of large‐size samples without the need for preprocessing. Significance and Impact of Study: The Spindle might be used to widely detaching micro‐organisms from all types of food samples for microbiological assay.     

Morphological differences between an artificial lentic and adjacent lotic environments in a characid species

Dam constructions cause fundamental changes in the natural landscape, creating new ecological and evolutionary challenges for aquatic organisms. In some cases, such water impoundments have been related with morphological changes in organisms. Understanding how populations respond to rapid environmental changes imposed by dams is the first step to elucidate the consequences that disturbed habitats may have on species evolution. In this work, we analyzed shape and size variation in Bryconamericus iheringii Boulenger 1887 from the Chasqueiro stream basin, south of Brazil, which was recently dammed. We used linear measurements and geometric morphometrics to identify morphological differences among specimens from the reservoir (lentic habitat) compared to the habitat upstream and downstream of the dam (lotic habitats). We also tested for size- and shape-related sexual dimorphism to determine whether variations observed were the same for both sexes. We found that B. iheringii from the artificial reservoir were distinct in shape and size to those from their natural habitat in the stream. The size variation between environments was the same for both sexes, but the shape variation differed between males and females. Regarding the linear measurements, lotic populations were larger (greater body length, width, pectoral fin base length and caudal peduncle length), probably in response to increased swimming activity. Regarding body shape, we found that both sexes have a more fusiform body in lotic habitats than in the reservoir. In addition, females showed an altered mouth position that was distinct between these environments. This work indicates that the water reservoir seems to be an important factor influencing morphological variation in B. iheringii, a species with sexual shape dimorphism.

     

精胺和Mg~（2＋）对tRNA~（Ile）圆二向色谱的影响

由于精胺（ｓｐｅｒｍｉｎｅ）能特异地刺激哺乳动物ｔＲＮＡ~（Ｉｌｅ）的氨基酰化,本文用纯化的牛肝ｔＲＮＡ~（Ｉｌｅ）观察了精胺和Ｍｇ（２＋）对ｔＲＮＡ~（Ｉｌｅ）ＣＤ光谱的影响。结果显示：Ｍｇ（２＋）可使牛肝ｔＲＮＡ~（Ｉｌｅ）ＣＤ光谱峰向短波方向偏移２ｎｍ,波峰为２６３ｎｍ,峰值被增大约１０％,ΔθＭｇ（２＋）＝２．３×１０３ｄｅｇ·ｃｍ２／ｄｍｏｌ;而精胺使牛肝ｔＲＮＡ~（Ｉｌｅ）ＣＤ光谱峰减少４０％,Δθｓｐｅｒｍｉｎｅ＝１×１０（－４）ｄｅｇ·ｃｍ２／ｄｍｏｌ;精胺和Ｍｇ（２＋）对肝ｔＲＮＡ~（Ｉｌｅ）－ＩｌｅＲＳ复合物或ＩｌｅＲＳ的ＣＤ光谱基本无影响。表明Ｍｇ（２＋）和精胺可影响牛肝ｔＲＮＡ~（Ｉｌｅ）的构象。实验同时以酵母ｔＲＮＡ（Ｐｈｅ）和Ｅ·ｃｏｌｉｔＲＮＡ~（Ｉｌｅ）作为对照。     

Partial characterization of transfer RNA genes isolated from Neurospora crassa

Summary Purified DNA sequences that code for tRNA in Neurospora crassa were isolated and partially characterized. The tRNA cistrons comprise about 0.3 percent of the N. crassa genome. The tRNA:tDNA hybrids showed a buoyant density in cesium sulfate of 1.48 g cm^-3 and sedimented in an intermediate position between native DNA and tRNA of N. crassa as expected. Te 50 of hybridized tRNA:tDNA molecules, reassociated tDNA: native DNA and homoduplexes of native DNA were 83.0°C, 88.5°C and 89.5°C respectively from thermal stability studies using hydroxyapatite chromatography. The isolated tRNA cistrons react almost completely with unlabeled DNA and tRNA of N. crassa or tRNA of the slime mutant of N. crassa; but react poorly with either ribosomal RNA or ribosomal RNA cistrons of N. crassa and tRNA of Escherichia coli. It appears that tRNA genes of N. crassa are repeated.This research was supported from grants from U.S. Atomic Energy Commission No. At(40-1)-4182 and the Anna Fuller Fund, New Haven, Connecticut to S.K.D. we are grateful to Dr. J. White, Director of H.U. Cancer Res. Center for help.