Translation initiation factors are not required for Dicistroviridae IRES function in vivo

The cricket paralysis virus (CrPV) intergenic region (IGR) internal ribosome entry site (IRES) uses an unusual mechanism of initiating translation, whereby the IRES occupies the P-site of the ribosome and the initiating tRNA enters the A-site. In vitro experiments have demonstrated that the CrPV IGR IRES is able to bind purified ribosomes and form 80S complexes capable of synthesizing small peptides in the absence of any translation initiation factors. These results suggest that initiation by this IRES is factor-independent. To determine whether the IGR IRES functions in the absence of initiation factors in vivo, we assayed IGR IRES activity in various yeast strains harboring mutations in canonical translation initiation factors. We used a dicistronic reporter assay in yeast to determine whether the CrPV IGR IRES is able to promote translation sufficient to support growth in the presence of various deletions or mutations in translation initiation factors. Using this assay, we have previously shown that the CrPV IGR IRES functions efficiently in yeast when ternary complexes (eIF2•GTP•initiator tRNA^met) are reduced. Here, we demonstrate that the CrPV IGR IRES activity does not require the eukaryotic initiation factors eIF4G1 or eIF5B, and it is enhanced when eIF2B, the eIF3b subunit of eIF3, or eIF4E are impaired. Taken together, these data support a model in which the CrPV IGR IRES is capable of initiating protein synthesis in the absence of any initiation factors in vivo, and suggests that the CrPV IGR IRES initiates translation by directly recruiting the ribosomal subunits in vivo.     

Characterization and properties of catalase immobilized onto controlled pore glass and its application in batch and plug-flow type reactors

Bovine liver catalase was covalently immobilized onto controlled pore glass (CPG) beads modified with 3-aminopropyltriethoxysilane (3-APTES) followed by treatment with glutaraldehyde. Coupling of catalase onto CPG was optimized to improve the efficiency of the overall immobilization procedure. The optimum coupling conditions: pore diameter of CPG, pH, buffer concentration, temperature, coupling time and initial catalase amount per grams of carrier were determined as 70 nm, 6.0, 75 mM, 5 °C, 7 h and 6 mg catalase, respectively. Catalytic efficiencies (k_cat/K_m) and thermal inactivation rate constants (k_i) of ICPG1 were determined and compared with that of free catalase. Suitability of ICPG1 was also investigated by using it in batch and plug-flow type reactors. When the remaining activity of ICPG1 retained was about 50% of its initial activity the highest total productivity of ICPG1 was determined as 7.6 × 10⁶ U g immobilized catalase⁻¹ in plug-flow type reactor. However, the highest total productivity of ICPG1 was 6.2 × 10⁵ U g immobilized catalase⁻¹ in batch type reactor. ICPG1 may have great potentials as biocatalyst for the application in decomposition of hydrogen peroxide in plug-flow type reactor.     

Karyotype variation within some native populations of oriental spruce (<Emphasis Type="Italic">Picea orientalis</Emphasis>) in Turkey

Karyological studies have been investigated within 8 native Anatolian populations of oriental spruce (Picea orientalis (L.) Link) in Turkey. The somatic chromosome number of 2n = 2x = 24 has been observed in all accessions. The karyotypes are generally asymmetrical with most of the chromosomes having median to median-submedian centromeres. Inter-population variability of the karyotype was summarized with cluster analysis. We found that the karyotypes have positively correlated with the altitudes of the natural habitats. The high value of karyotype asymmetry may be attributed to both microenvironment and natural regeneration methods used in oriental spruce.     

COMIT: identification of noncoding motifs under selection in coding sequences

Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences. We present the COMIT algorithm to detect functional noncoding motifs in coding regions using sequence conservation, explicitly separating nucleotide from amino acid effects. COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs. Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.     

Nitrogen and Phosphorus Limitation of Phytoplankton Growth in New Zealand Lakes: Implications for Eutrophication Control

We examine macronutrient limitation in New Zealand (NZ) lakes where, contrary to the phosphorus (P) only control paradigm, nitrogen (N) control is widely adopted to alleviate eutrophication. A review of published results of nutrient enrichment experiments showed that N more frequently limited lake productivity than P; however, stoichiometric analysis of a sample of 121 NZ lakes indicates that the majority (52.9%) of lakes have a mean ratio of total nitrogen (TN) to total phosphorus (TP) (by mass) indicative of potential P-limitation (>15:1), whereas only 14.0% of lakes have mean TN:TP indicative of potential N-limitation (<7:1). Comparison of TN, TP, and chlorophyll a data between 121 NZ lakes and 689 lakes in 15 European Union (EU) countries suggests that at the national scale, N has a greater role in determining lake productivity in NZ than in the EU. TN:TP is significantly lower in NZ lakes across all trophic states, a difference that is driven primarily by significantly lower in-lake TN concentrations at low trophic states and significantly higher TP concentrations at higher trophic states. The form of the TN:TP relationship differs between NZ and the EU countries, suggesting that lake nutrient sources and/or loss mechanisms differ between the two regions. Dual control of N and P should be the status quo for lacustrine eutrophication control in New Zealand and more effort is needed to reduce P inputs.     

Carbonic anhydrase inhibitory properties of some uracil derivatives

Inhibitors of carbonic anhydrase (CA) have been carried out in many therapeutic applications, especially antiglaucoma activity. In this study, we investigated some uracil derivatives (4–12) to inhibit human CA I (hCA I) and II (hCA II) isoenzymes. The K_I values of the compounds 4–12 are in the range of 0.085–428?µM for hCA I and of 0.1715–645?µM against hCA II, respectively. It is concluded from the kinetic investigations, all compounds used in the study act as competitive inhibitors with substrate, 4-NPA. Uracil derivatives are emerging agents for the inhibiton of carbonic anhydrase which could be used in biomedicine.     

Hypolimnetic phosphorus and nitrogen dynamics in a small,eutrophic lake with a seasonally anoxic hypolimnion

In situ estimates of sediment nutrient flux are necessary to understand seasonal variations in internal loading in lakes. We investigated the sources and sinks of nutrients in the hypolimnion of a small (0.33 km²), relatively shallow (18 m max. depth), eutrophic lake (Lake Okaro, New Zealand) in order to determine changes in sediment nutrient fluxes resulting from a whole lake sediment capping trial using a modified zeolite phosphorus inactivation agent (Z2G1). Sediment nutrient fluxes in the hypolimnion were estimated as the residual term in a nutrient budget model that accounted for mineralisation of organic nutrients, nutrient uptake by phytoplankton and mixing, nitrification, adsorption/desorption and diffusion of dissolved nutrients at the thermocline. Of the total hypolimnetic phosphate and ammonium fluxes during one period of seasonal stratification (2007–08), up to 60 and 50%, respectively, were derived from the bottom sediments, 18 and 24% were due to mineralisation of organic species, 36 and 28% were due to phytoplankton uptake and 9 and 6% were from diffusion across the thermocline. Adsorption/desorption of phosphate to suspended solids and nitrification were of minor (<8%) importance to the total fluxes. Any reduction in sediment nutrient release by Z2G1 was small compared with both the total sediment nutrient flux and the sum of other hypolimnetic fluxes. Uneven sediment coverage of Z2G1 may have been responsible for the limited effect of the sediment capping layer formed by Z2G1.     

Determination of stress responses induced by aluminum in maize (Zea mays)

To assess the alternative responses to aluminum toxicity, maize (Zea mays L. cv Karadeniz y?ld?z?) roots were exposed to different concentrations of AlCl3 (150, 300 and 450 μM). Aluminum reduced the root elongation by 39.6% in 150 μM, 44.1% in 300 μM, 50.1% in 450 μM AlCl3 after 96 h period. To correlate the root elongation with the alternative stress responses including aluminum accumulation, lipid peroxidation, mitotic abnormalities, reduction of starch content, intracellular Ca2+ accumulation, callose formation, lignin deposition and peroxidase activity, cytochemical and biochemical tests were performed. The results indicated that aluminum accumulation and lipid peroxidation were observed more densely on the root cap and the outer cortex cells. In addition to morphological deformations, cytochemical analysis displayed cellular deformations. Furthermore, mitotic abnormalities were observed such as c-mitosis, micronuclei, bi- and trinucleated cells in aluminum treated root tips. Aluminum treatment induced starch reduction, callose formation, lignin accumulation and intracellular Ca2+ increase. Moreover, the peroxidase activity increased significantly by 3, 4.4 and 7.7 times higher than in that of control after 96 h, respectively. In conclusion, aluminum is significantly stressful in maize culminating in morphological and cellular alterations.     

Mammalian retinal horizontal cells are unconventional GABAergic neurons

Lateral interactions at the first retinal synapse have been initially proposed to involve GABA by transporter-mediated release from horizontal cells, onto GABA(A) receptors expressed on cone photoreceptor terminals and/or bipolar cell dendrites. However, in the mammalian retina, horizontal cells do not seem to contain GABA systematically or to express membrane GABA transporters. We here report that mouse retinal horizontal cells express GAD65 and/or GAD67 mRNA, and were weakly but consistently immunostained for GAD65/67. While GABA was readily detected after intracardiac perfusion, it was lost during classical preparation for histology or electrophysiology. It could not be restored by incubation in a GABA-containing medium, confirming the absence of membrane GABA transporters in these cells. However, GABA was synthesized de novo from glutamate or glutamine, upon addition of pyridoxal 5'-phosphate, a cofactor of GAD65/67. Mouse horizontal cells are thus atypical GABAergic neurons, with no functional GABA uptake, but a glutamate and/or glutamine transport system allowing GABA synthesis, probably depending physiologically from glutamate released by photoreceptors. Our results suggest that the role of GABA in lateral inhibition may have been underestimated, at least in mammals, and that tissue pre-incubation with glutamine and pyridoxal 5'-phosphate should yield a more precise estimate of outer retinal processing.