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171.
Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat neglected area of molecular evolution. Escherichia coli, the first phylogenetic species for which more than two different strains have been sequenced, provides an invaluable framework to study the evolution of tRNA genes. In this work, a detailed analysis of the tRNA structure of the genomes of Escherichia coli strains K12, CFT073, and O157:H7, Shigella flexneri 2a 301, and Salmonella typhimurium LT2 was carried out. A phylogenetic analysis of these organisms was completed, and an archaeological map depicting the main events in the evolution of tRNA genes was drawn. It is shown that duplications, deletions, and horizontal gene transfers are the main factors driving tRNA evolution in these genomes. On average, 0.64 tRNA insertions/duplications occur every million years (Myr) per genome per lineage, while deletions occur at the slower rate of 0.30 per million years per genome per lineage. This work provides a first genomic glance at the problem of tRNA evolution as a repetitive process, and the relationship of this mechanism to genome evolution and codon usage is discussed. 相似文献
172.
Hundsrucker C Krause G Beyermann M Prinz A Zimmermann B Diekmann O Lorenz D Stefan E Nedvetsky P Dathe M Christian F McSorley T Krause E McConnachie G Herberg FW Scott JD Rosenthal W Klussmann E 《The Biochemical journal》2006,396(2):297-306
PKA (protein kinase A) is tethered to subcellular compartments by direct interaction of its regulatory subunits (RI or RII) with AKAPs (A kinase-anchoring proteins). AKAPs preferentially bind RII subunits via their RII-binding domains. RII-binding domains form structurally conserved amphipathic helices with unrelated sequences. Their binding affinities for RII subunits differ greatly within the AKAP family. Amongst the AKAPs that bind RIIalpha subunits with high affinity is AKAP7delta [AKAP18delta; K(d) (equilibrium dissociation constant) value of 31 nM]. An N-terminally truncated AKAP7delta mutant binds RIIalpha subunits with higher affinity than the full-length protein presumably due to loss of an inhibitory region [Henn, Edemir, Stefan, Wiesner, Lorenz, Theilig, Schmidtt, Vossebein, Tamma, Beyermann et al. (2004) J. Biol. Chem. 279, 26654-26665]. In the present study, we demonstrate that peptides (25 amino acid residues) derived from the RII-binding domain of AKAP7delta bind RIIalpha subunits with higher affinity (K(d)=0.4+/-0.3 nM) than either full-length or N-terminally truncated AKAP7delta, or peptides derived from other RII binding domains. The AKAP7delta-derived peptides and stearate-coupled membrane-permeable mutants effectively disrupt AKAP-RII subunit interactions in vitro and in cell-based assays. Thus they are valuable novel tools for studying anchored PKA signalling. Molecular modelling indicated that the high affinity binding of the amphipathic helix, which forms the RII-binding domain of AKAP7delta, with RII subunits involves both the hydrophobic and the hydrophilic faces of the helix. Alanine scanning (25 amino acid peptides, SPOT technology, combined with RII overlay assays) of the RII binding domain revealed that hydrophobic amino acid residues form the backbone of the interaction and that hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction. 相似文献
173.
Farooq SM Ebrahim AS Subramhanya KH Sakthivel R Rajesh NG Varalakshmi P 《Molecular and cellular biochemistry》2006,284(1-2):95-101
The assumption of oxidative stress as a mechanism in oxalate induced renal damage suggests that antioxidants might play a
beneficial role against oxalate toxicity. An in vivo model was used to investigate the effect of C-phycocyanin (from aquatic micro algae; Spirulina spp.), a known antioxidant, against calcium oxalate urolithiasis. Hyperoxaluria was induced in two of the 4 groups of Wistar albino
rats (n = 6 in each) by intraperitoneally injecting sodium oxalate (70,mg/kg body weight). A pretreatment of phycocyanin (100,mg/kg
body weight) as a single oral dosage was given, one hour prior to oxalate challenge. An untreated control and drug control
(phycocyanin alone) were employed. Phycocyanin administration resulted in a significant improvement (p < 0.001) in the thiol content of renal tissue and RBC lysate via increasing glutathione and reducing malondialdehyde levels
in the plasma of oxalate induced rats (p < 0.001), indicating phycocyanin’s antioxidant effect on oxalate mediated oxidative stress. Administering phycocyanin after
oxalate treatment significantly increased catalase and glucose-6-phosphate dehydrogenase activity (p < 0.001) in RBC lysate suggesting phycocyanin as a free radical quencher. Assessing calcium oxalate crystal retention in
renal tissue using polarization microscopy and renal ultrastructure by electron microscopy reveals normal features in phycocyanin
– pretreated groups. Thus the study presents positive pharmacological implications of phycocyanin against oxalate mediated
nephronal impairment and warrants further work to tap this potential aquatic resource for its medicinal application. (Mol
Cell Biochem xxx: 1–7, 2004) 相似文献
174.
RNA loop–loop interactions are a prevalent motif in the formation of tertiary structure and are well suited to trigger molecular recognition between RNA molecules. We determined the stabilities of several loop–loop interactions with a constant 6 bp core sequence and varying unpaired flanking nucleotides and found that the flanking bases have a strong influence on the stability and ion dependence of the kissing complex. In general, the stabilities determined in 1 M Na+ are equivalent to those in the presence of near physiological Mg2+ concentrations. Therefore we further tested whether the stabilities determined in vitro and within yeast cells correlate, using a recently developed yeast RNA-hybrid system. For the majority of the loop types analyzed here, the melting temperatures determined in vitro are in good agreement with the relative β-galactosidase activity in yeast cells, showing that data derived from in vitro measurements reflect in vivo properties. The most stable interactions are the naturally occurring HIV-1 DIS MAL and LAI derived loops with the motif (5′ AA/GN6A 3′), emphasizing the crucial role of stable kissing complexes in HIV genome dimerization. 相似文献
175.
176.
David P. J. Green Joel C. Trexler Jerome J. Lorenz Carole C. McIvor Tom Philippi 《Hydrobiologia》2006,569(1):387-399
In tropical and subtropical estuaries, gradients of primary productivity and salinity are generally invoked to explain patterns
in community structure and standing crops of fishes. We documented spatial and temporal patterns in fish community structure
and standing crops along salinity and nutrient gradients in two subtropical drainages of Everglades National Park, USA. The
Shark River drains into the Gulf of Mexico and experiences diurnal tides carrying relatively nutrient enriched waters, while
Taylor River is more hydrologically isolated by the oligohaline Florida Bay and experiences no discernable lunar tides. We
hypothesized that the more nutrient enriched system would support higher standing crops of fishes in its mangrove zone. We
collected 50 species of fish from January 2000 to April 2004 at six sampling sites spanning fresh to brackish salinities in
both the Shark and Taylor River drainages. Contrary to expectations, we observed lower standing crops and density of fishes
in the more nutrient rich tidal mangrove forest of the Shark River than in the less nutrient rich mangrove habitats bordering
the Taylor River. Tidal mangrove habitats in the Shark River were dominated by salt-tolerant fish and displayed lower species
richness than mangrove communities in the Taylor River, which included more freshwater taxa and yielded relatively higher
richness. These differences were maintained even after controlling for salinity at the time of sampling. Small-scale topographic
relief differs between these two systems, possibly created by tidal action in the Shark River. We propose that this difference
in topography limits movement of fishes from upstream marshes into the fringing mangrove forest in the Shark River system,
but not the Taylor River system. Understanding the influence of habitat structure, including connectivity, on aquatic communities
is important to anticipate effects of construction and operational alternatives associated with restoration of the Everglades
ecosystem. 相似文献
177.
In the present study, we studied epithelial-mesenchymal transition (EMT) with fetal and postnatal serial skin sections. E-cadherin, occludin and zonula occludens 1 (ZO-1)-expressing cells appear in the dermal area from E18.5 to postnatal day 9 (P9), with highest expression from P2 to P5. The co-expression of mesenchymal marker alpha-smooth muscle (alpha-SMA), fibronectin and vimentin with E-cadherin in these dermal cells was further examined. Almost no dermal cells express alpha-SMA before P0. From P2 to P6, cells expressing both E-cadherin and alpha-SMA appear in the dermis. In contrast, fibronectin-releasing cells were detected in the dermis as early as on E15.5, although on P5, some dermal cells was found weakly expressing both fibronectin and E-cadherin, most cells strongly expressing fibronectin did not express E-cadherin. Vimentin was mainly expressed in both endothelial and blood-derived cells and did not show co-expression with E-cadherin. Confocal microscopy studies further found that during EMT, E-cadherin appears intracellularly, while the expression of alpha-SMA starts from the membrane area and moves to the cytosol of the cells. Our data are the first in vivo evidence that EMT occurs during mouse skin development. Dermal cells are derived from EMT and other origins, including blood, during skin development. 相似文献
178.
Campbell JL Lorenz A Witkin KL Hays T Loidl J Cohen-Fix O 《Molecular biology of the cell》2006,17(4):1768-1778
Little is known about what dictates the round shape of the yeast Saccharomyces cerevisiae nucleus. In spo7Delta mutants, the nucleus is misshapen, exhibiting a single protrusion. The Spo7 protein is part of a phosphatase complex that represses phospholipid biosynthesis. Here, we report that the nuclear protrusion of spo7Delta mutants colocalizes with the nucleolus, whereas the nuclear compartment containing the bulk of the DNA is unaffected. Using strains in which the nucleolus is not intimately associated with the nuclear envelope, we show that the single nuclear protrusion of spo7Delta mutants is not a result of nucleolar expansion, but rather a property of the nuclear membrane. We found that in spo7Delta mutants the peripheral endoplasmic reticulum (ER) membrane was also expanded. Because the nuclear membrane and the ER are contiguous, this finding indicates that in spo7Delta mutants all ER membranes, with the exception of the membrane surrounding the bulk of the DNA, undergo expansion. Our results suggest that the nuclear envelope has distinct domains that differ in their ability to resist membrane expansion in response to increased phospholipid biosynthesis. We further propose that in budding yeast there is a mechanism, or structure, that restricts nuclear membrane expansion around the bulk of the DNA. 相似文献
179.
The need to identify “toxicologically equivalent” doses across different species is a major issue in toxicology and risk assessment. In this article, we describe an approach for establishing default cross-species extrapolation factors used to scale oral doses across species for non-carcinogenic endpoints. This work represents part of an on-going effort to harmonize the way animal data are evaluated for carcinogenic and non-carcinogenic endpoints. In addition to considering default scaling factors, we also discuss how chemical-specific data (e.g., metabolic or mechanistic data) can be incorporated into the dose extrapolation process. After first examining the required properties of a default scaling methodology, we consider scaling approaches based on empirical relationships observed for particular classes of compounds and also more theoretical approaches based on general physiological principles (i.e, allometry). The available data suggest that the empirical and allometric approaches each provide support for the idea that toxicological risks are approximately equal when daily oral doses are proportional to body weight raised to the 3/4-power. We also discuss specific challenges for dose scaling related to different routes of exposure, acute versus chronic toxicity, and extrapolations related to particular life stages (e.g., childhood). 相似文献
180.
Klumpp M Boettcher A Becker D Meder G Blank J Leder L Forstner M Ottl J Mayr LM 《Journal of biomolecular screening》2006,11(6):617-633
This article discusses the development of homogeneous, miniaturized assays for the identification of novel kinase inhibitors from very large compound collections. In particular, the suitability of time-resolved fluorescence resonance energy transfer (TR-RET) based on phospho-specific antibodies, an antibody-independent fluorescence polarization (FP) approach using metal-coated beads (IMAP technology), and the determination of adenosine triphosphate consumption through chemiluminescence is evaluated. These readouts are compared with regard to assay sensitivity, compound interference, reagent consumption, and performance in a 1536-well format, and practical considerations for their application in primary screening or in the identification of kinase substrates are discussed. All of the tested technologies were found to be suitable for miniaturized high-throughput screening (HTS) in principle, but each of them has distinct limitations and advantages. Therefore, the target-specific selection of the most appropriate readout technology is recommended to ensure maximal relevance of HTS campaigns. 相似文献