Human Cells Have a Limited Set of tRNA Anticodon Loop Substrates of the tRNA Isopentenyltransferase TRIT1 Tumor Suppressor

Human TRIT1 is a tRNA isopentenyltransferase (IPTase) homologue of Escherichia coli MiaA, Saccharomyces cerevisiae Mod5, Schizosaccharomyces pombe Tit1, and Caenorhabditis elegans GRO-1 that adds isopentenyl groups to adenosine 37 (i6A37) of substrate tRNAs. Prior studies indicate that i6A37 increases translation fidelity and efficiency in codon-specific ways. TRIT1 is a tumor suppressor whose mutant alleles are associated with cancer progression. We report the systematic identification of i6A37-containing tRNAs in a higher eukaryote, performed using small interfering RNA knockdown and other methods to examine TRIT1 activity in HeLa cells. Although several potential substrates contained the IPTase recognition sequence A36A37A38 in the anticodon loop, only tRNA^SerAGA, tRNA^SerCGA, tRNA^SerUGA, and selenocysteine tRNA with UCA (tRNA^[Ser]SecUCA) contained i6A37. This subset is a significantly more restricted than that for two distant yeasts (S. cerevisiae and S. pombe), the only other organisms comprehensively examined. Unlike the fully i6A37-modified tRNAs for Ser, tRNA^[Ser]SecUCA is partially (∼40%) modified. Exogenous selenium and other treatments that decreased the i6A37 content of tRNA^[Ser]SecUCA led to increased levels of the tRNA^[Ser]SecUCA. Of the human mitochondrion (mt)-encoded tRNAs with A36A37A38, only mt tRNAs tRNA^SerUGA and tRNA^TrpUCA contained detectable i6A37. Moreover, while tRNA^Ser levels were unaffected by TRIT1 knockdown, the tRNA^[Ser]SecUCA level was increased and the mt tRNA^SerUGA level was decreased, suggesting that TRIT1 may control the levels of some tRNAs as well as their specific activity.     

Biotransformation of benzonitrile herbicides via the nitrile hydratase–amidase pathway in rhodococci

The aim of this work was to determine the ability of rhodococci to transform 3,5-dichloro-4-hydroxybenzonitrile (chloroxynil), 3,5-dibromo-4-hydroxybenzonitrile (bromoxynil), 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) and 2,6-dichlorobenzonitrile (dichlobenil); to identify the products and determine their acute toxicities. Rhodococcus erythropolis A4 and Rhodococcus rhodochrous PA-34 converted benzonitrile herbicides into amides, but only the former strain was able to hydrolyze 2,6-dichlorobenzamide into 2,6-dichlorobenzoic acid, and produced also more of the carboxylic acids from the other herbicides compared to strain PA-34. Transformation of nitriles into amides decreased acute toxicities for chloroxynil and dichlobenil, but increased them for bromoxynil and ioxynil. The amides inhibited root growth in Lactuca sativa less than the nitriles but more than the acids. The conversion of the nitrile group may be the first step in the mineralization of benzonitrile herbicides but cannot be itself considered to be a detoxification.     

The effect of venous thromboembolism on survival of cancer patients and its relationship with serum levels of factor VIII and vascular endothelial growth factor: a prospective matched-paired study

BACKGROUND: Venous thromboembolism (VT) increases mortality and morbidity in cancer patients. The primary aim of this study was to evaluate the effect of VT on the survival of cancer patients and its relationship with serum vascular endothelial growth factor (VEGF) and plasma factor VIII levels. PATIENTS AND METHODS: Eighty-two patients with locally advanced or metastatic cancer were included in this study between September 2001 and March 2004, and 31 of them had VT. Fifty-one matched-paired cancer patients without VT were prospectively selected as a control group in the same period. Criteria for the selection of control group patients were having the same malignancy, stage, metastatic site, performance status and age (+/-5 years) as patients in the VT group. RESULTS: Plasma factor VIII and serum D-dimer levels in the VT group were significantly higher than those in the control group (p=0.030 and p=0.016, respectively). However, mean serum VEGF levels were similar in both groups (p=0.199). In the VT group, the median survival of patients who had higher serum VEGF levels (>150 pg/mL) was significantly shorter than that of patients in the same group with lower serum VEGF levels (p=0.005). The median survival of the VT group was 14 months, whereas it was 25 months in the control group (p=0.199). CONCLUSION: There was a worse prognostic trend for cancer patients with VT. Nevertheless, the difference in survival was not statistically significant between the groups. Plasma factor VIII and serum D-dimer levels might have prognostic value in cancer patients with VT. Cancer patients with VT and higher serum VEGF levels had a significantly poorer prognosis.     

Two new genera,Caveana gen. nov. and Triviola gen. nov., and two new Torodora species from Thailand (Lepidoptera: Lecithoceridae)

Two new genera, Caveana, gen. nov. and Triviola, gen. nov., belonging to the subfamily Torodorinae (Lecithoceridae) are described, based on Caveana diemseoki, sp. nov. and Triviola puiensis, sp. nov. At the same time, two new Torodora species, T. karismata, sp. nov. and T. youwon, sp. nov., are also described from Thailand. Images of adults and genitalia are given.     

Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes

Background  

Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species and can be grouped into microsatellite-associated DNA families. These families are thought to be associated with unequal crossing-over during DNA recombination or with transposable elements (TEs).     

Seasonal succession of zooplankton in the north basin of Lake Biwa

To examine the seasonal succession of the entire zooplankton community in Lake Biwa, zooplankton biomass (on an areal basis) and its distribution patterns among crustaceans, rotifers and ciliates were studied in the north basin from April 1997 to June 1998. Seasonal changes in phytoplankton and population dynamics of Daphnia galeata were also examined to assess food condition and predation pressure by fish. From March to November, crustaceans dominated zooplankton biomass, but rotifers and ciliates were dominant from December to February. Among crustaceans, Eodiaptomus japonicus was the most abundant species, followed by D. galeata. Zooplankton biomass increased from January to a peak in early April, just before the spring bloom of phytoplankton, then decreased in mid-April when mortality rate of D. galeata increased. From mid-June, zooplankton increased and maintained a high level until the beginning of November. During this period, both birth and mortality rates of D. galeata were relatively high and a number of rotifer and crustacean species were observed. However, their abundances were very limited except for E. japonicus which likely preys on ciliates and rotifers. In Lake Biwa, food sources other than phytoplankton, such as resuspended organic matter from the sediments, seems to play a crucial role in zooplankton succession from winter to early spring, while zooplankton community seems to be regulated mainly by fish predation from summer to fall.     

Acrylamide synthesis using agar entrapped cells of <Emphasis Type="Italic">Rhodococcus rhodochrous</Emphasis> PA-34 in a partitioned fed batch reactor

The nitrile hydratase (Nhase) induced cells of Rhodococcus rhodochrous PA-34 catalyzed the conversion of acrylonitrile to acrylamide. The cells of R. rhodochrous PA-34 immobilized in 2% (w/v) agar (1.76 mg dcw/ml agar matrix) exhibited maximum Nhase activity (8.25 U/mg dcw) for conversion of acrylonitrile to acrylamide at 10°C in the reaction mixture containing 0.1 M potassium phosphate buffer (pH 7.5), 8% (w/v) acrylonitrile and immobilized cells equivalent to 1.12 mg dcw (dry cell weight) per ml. In a partitioned fed batch reaction at 10°C, using 1.12 g dcw immobilized cells in a final volume of 1 l, a total of 372 g of acrylonitrile was completely hydrated to acrylamide (498 g) in 24 h. From the above reaction mixture 87% acrylamide (432 g) was recovered through crystallization at 4°C. By recycling the immobilized biocatalyst (six times), a total of 2,115 g acrylamide was produced.     

Role of phytoplankton size distribution in lake ecosystems revealed by a comparison of whole plankton community structure between Lake Baikal and Lake Biwa

The influence of the size distribution of phytoplankton on changes in the planktonic food web structures with eutrophication was examined using natural planktonic communities in two world-famous lakes: Lake Baikal and Lake Biwa. The size distribution of phytoplankton and the ratio of heterotrophic to autotrophic biomass (H/A ratio), indicating the balance between primary production and its consumption, were investigated in the lakes of different trophic status. The results revealed that microphytoplankton (>20μm) in mesotrophic Lake Biwa, and picophytoplankton (<2μm) or nanophytoplankton (2–20μm) in oligotrophic Lake Baikal, comprised the highest proportion of the total phytoplankton biomass. The H/A ratio was lower in Lake Biwa (<1) than in Lake Baikal (>1). The low H/A ratio in Lake Biwa appeared to be the consequence of the lack of consumption of the more abundant microphytoplankton, which were inferior competitors in nutrient uptake under oligotrophic conditions but less vulnerable to grazing. As a result, unconsumed microphytoplankton accumulated in the water column, decreasing the H/A ratio in Lake Biwa. Our results showed that food web structure and energy flow in planktonic communities were greatly influenced by the size distribution of phytoplankton, in conjunction with bottom-up (nutrient uptake) and top-down (grazing) effects at the trophic level of primary producers.     

Lack of tRNA Modification Isopentenyl-A37 Alters mRNA Decoding and Causes Metabolic Deficiencies in Fission Yeast

tRNA isopentenyltransferases (Tit1) modify tRNA position 37, adjacent to the anticodon, to N⁶-isopentenyladenosine (i6A37) in all cells, yet the tRNA subsets selected for modification vary among species, and their relevance to phenotypes is unknown. We examined the function of i6A37 in Schizosaccharomyces pombe tit1⁺ and tit1-Δ cells by using a β-galactosidase codon-swap reporter whose catalytic activity is sensitive to accurate decoding of codon 503. i6A37 increased the activity of tRNA^Cys at a cognate codon and that of tRNA^Tyr at a near-cognate codon, suggesting that i6A37 promotes decoding activity generally and increases fidelity at cognate codons while decreasing fidelity at noncognate codons. S. pombe cells lacking tit1⁺ exhibit slow growth in glycerol or rapamycin. While existing data link wobble base U34 modifications to translation of functionally related mRNAs, whether this might extend to the anticodon-adjacent position 37 was unknown. Indeed, we found a biased presence of i6A37-cognate codons in high-abundance mRNAs for ribosome subunits and energy metabolism, congruent with the observed phenotypes and the idea that i6A37 promotes translational efficiency. Polysome profiles confirmed the decreased translational efficiency of mRNAs in tit1-Δ cells. Because subsets of i6A37-tRNAs differ among species, as do their cognate codon-sensitive mRNAs, these genomic variables may underlie associated phenotypic differences.     

The centromeric regions of potato chromosomes contain megabase-sized tandem arrays of telomere-similar sequence

Telomere-similar sequences have been found in non-telomeric regions in various eukaryotic species. Centromeric regions often harbor such interstitial telomeric repeats (ITRs). We isolated a 2.8 kb ITR, pSbTC1, in a diploid potato species Solanum bulbocastanum. DNA sequences related to the pSbTC1 family are widely distributed in different Solanum species. The pSbTC1-related sequences are organized into tandem arrays and located mainly in the centromeric regions of potato chromosomes. Most notably, the pSbTC1-related sequences have undergone extensive amplification and a single array can span up to multiple megabases. These results suggest that the pSbTC1-related sequences are not simple relics of ancient events in karyotype evolution, such as chromosomal fusions. We also demonstrated that the pSbTC1-related sequences are heavily methylated and are associated with highly condensed centromeric heterochromatin.