Role of Aromatic Amino-acid Residues in the Binding of Enzymes and Proteins to Nucleic Acids

MANY studies have been made of the specificity of interaction between nucleic acids and polypeptides, proteins and enzymes^1,2. Electrostatic forces between basic amino-acids and phosphate groups contribute to the stability of the complexes, but selective recognition requires more specific interactions which are not yet understood. The recognition of a specific region of a nucleic acid could be explained if this region has some particular conformation or if there are specific interactions between a few amino-acid residues and the bases of this region. We wish to report results which show that the aromatic amino-acids tryptophan and tyrosine can interact with nucleic acid bases in double stranded nucleic acids. They suggest that aromatic amino-acid residues of enzymes and proteins could participate in the binding to nucleic acids by intercalating between the bases and thus constraining the nucleic acid molecule to adopt a definite position with respect to the protein molecule.     

A new species of Dyrosaurus (Crocodylomorpha, Dyrosauridae) from the early Eocene of Morocco: phylogenetic implications

A new dyrosaurid is described from the Ypresian of the phosphatic deposits of the Oulad Abdoun Basin of Morocco. It is based on numerous cranial and postcranial remains, allowing an almost complete reconstruction. This new Dyrosaurus species, Dyrosaurus maghribensis sp. nov. , is currently only known from Morocco. It differs from D. phosphaticus , present in contemporaneous levels of Algeria and Tunisia, by several autapomorpies, including a smooth dorsal margin of the parietal and widely opened choanae. A phylogenetic analysis, using 47 taxa and 234 morphological characters, shows the dyrosaurids as the sister taxon of pholidosaurids, which include Elosuchus , Sarcosuchus , Terminonaris and Pholidosaurus , and the thalattosuchians. Goniopholididae is a non-monophyletic group; however, if dyrosaurids are not included in the analysis, the result differs and the goniopholidids form a distinct clade. If Thalattosuchia is excluded, both Goniopholididae and Pholidosauridae become paraphyletic assemblages. Thus, phylogenetic problems remain with respect to longirostrine clade, and more attention should be paid to resolving their evolutionary relationships amongst the crocodyliforms.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 603–656.     

The Leeds Evaluation of Efficacy of Detoxification Study (LEEDS) Prisons Project Study: protocol for a randomised controlled trial comparing methadone and buprenorphine for opiate detoxification

Many research-funding agencies now require open access to the results of research they have funded, and some also require that researchers make available the raw data generated from that research. Similarly, the journal Trials aims to address inadequate reporting in randomised controlled trials, and in order to fulfil this objective, the journal is working with the scientific and publishing communities to try to establish best practice for publishing raw data from clinical trials in peer-reviewed biomedical journals. Common issues encountered when considering raw data for publication include patient privacy – unless explicit consent for publication is obtained – and ownership, but agreed-upon policies for tackling these concerns do not appear to be addressed in the guidance or mandates currently established. Potential next steps for journal editors and publishers, ethics committees, research-funding agencies, and researchers are proposed, and alternatives to journal publication, such as restricted access repositories, are outlined.     

Sediment accumulation predicts the distribution of a unionid mussel (Elliptio complanata) in nearshore areas of a Canadian Shield lake

1. The importance of native freshwater mussels for ecosystem processes depends on their density, size distribution and activity. In lakes, many of the factors that affect mussels (fish hosts, habitat, food) could be directly or indirectly related to wind‐driven physical processes. 2. We tested whether the abundance and size of Elliptio complanata in the shallow, nearshore areas of a medium‐sized lake were related to site exposure, substratum type and fish distribution. To disentangle some of the correlated variables known to affect mussel distribution, we used paired exposed and sheltered sampling sites along the 7‐km fetch of the lake basin. 3. The distribution of sediment characteristics in nearshore areas was highly predictable. The mean depth of accumulated soft sediments decreased with increasing fetch at wind‐exposed sites, but increased with increasing fetch at sheltered sites. Sediments were deeper along the main shoreline than around islands. Deeper sediments tended to be finer and higher in silt content and organic fraction. 4. The density and proportion of juvenile mussels along the main shoreline varied in a unimodal way with sediment depth. These results suggest that wind‐driven physical forces affect the transport of young juveniles to sediment depositional areas and create sediment conditions that influence their growth and survival. In contrast, the proportion of juvenile mussels around islands was not related to sediment characteristics, but decreased with remoteness of the island, suggesting that the distribution of juvenile mussels may be limited by fish movements. These results are tentative since they do not include buried juvenile mussels. 5. We also found a unimodal relationship between total mussel density (juveniles and adults) and sediment depth but, in contrast to the relationship for juveniles only, it applied to all sites with soft sediments, including islands. We conclude that factors related to sediment depth affect the growth and survival of adult mussels around islands and that these factors are strong enough to modify the pattern of distribution established via dispersal during earlier life stages. 6. The mean shell length of adults at different sites within the lake basin ranged from 60 to 85 mm. Mussel shell length decreased with increasing fetch at sites exposed to the prevalent winds, but was relatively constant on the sheltered side of peninsulas and islands. The size of unionid mussels in different parts of the lake seems to be determined both by their exposure to physical forces and by sediments. 7. The local distribution of E. complanata is determined, directly and indirectly, by wind‐driven forces. These processes are likely to be important for other benthic organisms affected by similar habitat conditions (e.g. sediment characteristics, physical disturbance).     

The eIF1A C-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo

Translation initiation factor 1A stimulates 40S-binding of the eukaryotic initiation factor 2 (eIF2)/GTP/Met-tRNA(iMet) ternary complex (TC) and promotes scanning in vitro. eIF1A contains an OB-fold present in bacterial IF1 plus N- and C-terminal extensions. Truncating the C-terminus (deltaC) or mutating OB-fold residues (66-70) of eIF1A reduced general translation in vivo but increased GCN4 translation (Gcd- phenotype) in a manner suppressed by overexpressing TC. Consistent with this, both mutations diminished 40S-bound TC, eIF5 and eIF3 in vivo, and deltaC impaired TC recruitment in vitro. The assembly defects of the OB-fold mutation can be attributed to reduced 40S-binding of eIF1A, whereas deltaC impairs eIF1A function on the ribosome. A substitution in the C-terminal helix (98-101) also reduced 43S assembly in vivo. Rather than producing a Gcd- phenotype, however, 98-101 impairs GCN4 derepression in a manner consistent with defective scanning by reinitiating ribosomes. Indeed, 98-101 allows formation of aberrant 48S complexes in vitro and increases utilization of non-AUG codons in vivo. Thus, the OB-fold is crucial for ribosome-binding and the C-terminal domain of eIF1A has eukaryotic-specific functions in TC recruitment and scanning.     

Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites

Two exceptional mechanisms of eukaryotic translation initiation have recently been identified that differ fundamentally from the canonical factor-mediated, end-dependent mechanism of ribosomal attachment to mRNA. Instead, ribosomal 40S subunits bind in a factor-independent manner to the internal ribosomal entry site (IRES) in an mRNA. These two mechanisms are exemplified by initiation on the unrelated approximately 300 nt.-long Hepatitis C virus (HCV) IRES and the approximately 200 nt.-long cricket paralysis virus (CrPV) intergenic region (IGR) IRES, respectively. Ribosomal binding involves interaction with multiple non-contiguous sites on these IRESs, and therefore also differs from the factor-independent attachment of prokaryotic ribosomes to mRNA, which involves base-pairing to the linear Shine-Dalgarno sequence. The HCV IRES binds to the solvent side of the 40S subunit, docks a domain of the IRES into the ribosomal exit (E) site and places the initiation codon in the ribosomal peptidyl (P) site. Subsequent binding of eIF3 and the eIF2-GTP/initiator tRNA complex to form a 48S complex is followed by subunit joining to form an 80S ribosome. The CrPV IRES binds to ribosomes in a very different manner, by occupying the ribosomal E and P sites in the intersubunit cavity, thereby excluding initiator tRNA. Ribosomes enter the elongation stage of translation directly, without any involvement of initiator tRNA or initiation factors, following recruitment of aminoacyl-tRNA to the ribosomal aminoacyl (A) site and translocation of it to the P site.     

Variety-specific actinomycete complexes associated with barley roots in soddy podzolic soil

The root-colonizing actinomycete complexes of genotypically different barley plants grown in soddy podzolic soil were found to contain streptomycetes of the sections Cinereus (series Chromogenes, Achromogenes, and Aureus) and Roseus (series Fradiae), dominant being streptomycetes of the section Cinereus ser. Chromogenes. The abundance and diversity of soil streptomycetes in the barley rhizoplane increased in the order: var. 999-93 < var. Kumir < var. Novichok < var. 889-93. Experiments revealed functional specificity in the root-associated actinomycete complexes of different barley varieties. The actinomycete complex colonizing the barley var. 999-93 roots was distinguished by a wide range of utilizable root exudate metabolites and a low occurrence rate of antagonistic species.     

Factors Mediating the Vitamin B12 Requirement of Euglena

SYNOPSIS. Deprived of vitamin B₁₂, Euglena gracilis strain Z ceases to divide which we believe to be a function of the light regime: division inhibition occurs more quickly in continuous light than in alternating (6L : 6D) light and not at all in total darkness. This phenomenon is dependent on the carbon source; cells grown in glutamate-malate medium do not divide regardless of the culture conditions while dl -lactate as carbon source permits growth in darkness in the absence of B₁₂. Conditions which lead to an increased O₂ or decreased CO₂ tension in the medium, such as agitation in darkness or incubation in red or white light, result in inhibition of division. This inhibition can be reversed by re-transferring the cells to still culture in the dark or, in the case of light-induced blockage, by the addition of DCMU.     

A diminution in ascorbate oxidase activity affects carbon allocation and improves yield in tomato under water deficit

The regulation of carbon allocation between photosynthetic source leaves and sink tissues in response to stress is an important factor controlling plant yield. Ascorbate oxidase is an apoplastic enzyme, which controls the redox state of the apoplastic ascorbate pool. RNA interference was used to decrease ascorbate oxidase activity in tomato (Solanum lycopersicum L.). Fruit yield was increased in these lines under three conditions where assimilate became limiting for wild‐type plants: when fruit trusses were left unpruned, when leaves were removed or when water supply was limited. Several alterations in the transgenic lines could contribute to the improved yield and favour transport of assimilate from leaves to fruits in the ascorbate oxidase lines. Ascorbate oxidase plants showed increases in stomatal conductance and leaf and fruit sugar content, as well as an altered apoplastic hexose : sucrose ratio. Modifications in gene expression, enzyme activity and the fruit metabolome were coherent with the notion of the ascorbate oxidase RNAi lines showing altered sink strength. Ascorbate oxidase may therefore be a target for strategies aimed at improving water productivity in crop species.