Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for the propagation of coronaviruses. The combination of genomic features that make up PFE—the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements—places severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess the evolutionary dynamics of PFE in great detail. Here, we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and ORF1b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well-defined phylogenetic specificity. We further examined sequencing data from over 1,500,000 complete genomes and 55,000 raw read data sets to demonstrate exceptional conservation and detect signatures of selection within the PFE region.     

A wave of free cytosolic calcium traverses zebrafish eggs on activation.

The activation process in a variety of deuterostome and protostome eggs is accompanied by cytosolic calcium transients that usually take the form of either a single or multiple propagating waves. Here we report that the eggs of zebrafish (Danio rerio) are no exception in that they generate a single activation wave that traverses the egg at a velocity of around 9 microm/s. There appears, however, to be no difference between the calcium-mediated activation response of eggs with regard to the presence or absence of sperm in the spawning medium. This leads us to suggest that these eggs are normally activated when they come in contact with their spawning medium and are then subsequently fertilized. The aspermic wave is initiated at the animal pole in the region of the micropyle, appears to propagate mainly through the yolk-free egg cortex, and then terminates at the vegetal pole. As neither sperm nor external calcium is required for the initiation (or propagation) of the activation wave, this suggests that an alternative wave trigger must be involved.     

Translation initiation factor 3 antagonizes authentic start codon selection on leaderless mRNAs

In this study, we have examined the influence of initiation factors on translation initiation of leaderless mRNAs whose 5'-terminal residues are the A of the AUG initiating codon. A 1:1 ratio of initiation factors to ribosomes abolished ternary complex formation at the authentic start codon of different leaderless mRNAs. Supporting this observation, in vitro translation assays using limiting ribosome concentrations with competing leaderless λ c I and Escherichia coli ompA mRNAs, the latter containing a canonical ribosome binding site, revealed reduced cI synthesis relative to OmpA in the presence of added initiation factors. Using in vitro toeprinting and in vitro translation assays, we show that this effect can be attributed to IF3. Moreover, in vivo studies revealed that the translational efficiency of a leaderless reporter gene is decreased with increased IF3 levels. These studies are corroborated by the observed increased translational efficiency of a leaderless reporter construct in an infC mutant strain unable to discriminate against non-standard start codons. These results suggest that, in the absence of a leader or a Shine–Dalgarno sequence, the function(s) of IF3 limits stable 30S ternary complex formation.     

Effects of prolonged iron loading in the rat using both parenteral and dietary routes.

Female Porton rats have been treated with either parenteral iron (intraperitoneal red cells) or dietary iron (carbonyl iron) for up to 12 months or 22 months respectively. In the parenteral iron loaded animals, the liver iron concentration rose from approximately 2 mg g^-1 dry wt at 2 months to 21 mg g^-1 dry wt at 12 months, while for the dietary iron loaded animals, this value rose from 14 to 48 mg g^-1 dry wt at 12 months to over 60 mg g^-1 dry wt after 22 months. In contrast, splenic iron concentrations rose more in the parenterally loaded animals (up to 66 mg g-1 dry wt after 12 months) than in the dietary loaded animals (approx. 34 mg g^-1 dry wt after 24 months). This study yielded hepatic iron concentrations comparable to those seen in human thalassaemia patients with comparative low hepatotoxicity. Splenic iron concentrations in the parenteral iron loaded group generally exceeded those reported in thalassaemia. Iron concentrations derived from computer assisted morphometry of liver iron deposits correlated well ( r = 0.88, p < 0.001) with chemical analysis data. The fraction of iron in the non-parenchymal cells correlated positively with the duration of iron loading (r = 0.86, p < 0.001).     

Separation and quantification of ropinirole and some impurities using capillary liquid chromatography

Ropinirole, 4-[2-(dipropylamino)ethyl]-1,3-dihydro-2H-indol-2-one, is a potent anti-Parkinson’s disease drug developed by SmithKline Beecham Pharmaceuticals. Capillary liquid chromatography (CLC) was used for the separation and quantification of ropinirole and its five related impurities, potentially formed during its synthesis. A simultaneous optimization of three mobile phase parameters, i.e., pH, buffer concentration and acetonitrile content was performed employing an experimental design approach which proved a powerful tool in method development. The retention factors of the investigated substances in different mobile phases were determined. Baseline resolution of the six substances on a C₁₈ reversed stationary phase was attained using a mobile phase with an optimized composition [acetonitrile–8.7 mM 2-(N-morpholino)ethanesulfonic acid adjusted to pH 6.0 (55:45, v/v)]. It was shown that CLC, operated in the isocratic mode under the mobile phase flow-rate of 4 μl/min, can determine the level of these impurities, down to a level of 0.06% of the main component within 25 min.     

ATPase and shortening rates in frog fast skeletal myofibrils by time-resolved measurements of protein-bound and free Pi.

Shortening and ATPase rates were measured in Ca2+-activated myofibrils from frog fast muscles in unloaded conditions at 4 degrees C. ATPase rates were determined using the phosphate-binding protein method (free phosphate) and quench flow (total phosphate). Shortening rates at near zero load (V0) were estimated by quenching reaction mixtures 50 ms to 10 s old at pH 3.5 and measuring sarcomere lengths under the optical microscope. As with the rabbit psoas myofibrils (C. Lionne, F. Travers, and T. Barman, 1996, Biophys. J. 70:887-895), the ATPase progress curves had three phases: a transient Pi burst, a fast linear phase (kF), and a deceleration to a slow phase (kS). Evidence is given that kF is the ATPase rate of shortening myofibrils. V0 is in good agreement with mechanical measurements in myofibrils and fibers. Under the same conditions and at saturation in ATP, V0 and kF are 2.4 microm half-sarcomere(-1) s(-1) and 4.6 s(-1), and their Km values are 33 and 200 microM, respectively. These parameters are higher than found with rabbit psoas myofibrils. The myofibrillar kF is higher than the fiber ATPase rates obtained previously in frog fast muscles but considerably lower than obtained in skinned fibers by the phosphate-binding protein method (Z. H. He, R. K. Chillingworth, M. Brune, J. E. T. Corrie, D. R. Trentham, M. R. Webb, and M. R. Ferenczi, 1997, J. Physiol. 50:125-148). We show that, with frog as with rabbit myofibrillar ATPase, phosphate release is the rate-limiting step.     

Effects of topography on rainforest tree community structure and diversity in American Samoa, and implications for frugivore and nectarivore populations

Aim We investigated the spatial variation of rainforest tree community structure and composition to determine if forest structure and diversity varied as a function of topography; and in turn if this could influence patterns of habitat use by native forest birds and pteropodid bats. Location The study was undertaken on the island of Tutuila, American Samoa, located in the South Pacific Ocean. Methods All trees ≥10 cm diameter were censused in sixty 200 m² plots in ridge, slope and valley forest across the island of Tutuila. Results Forest structure varied significantly across topographical space. Ridge forest was shortest and had the highest stem densities, and valley forest was tallest with the fewest stems per unit area. Species richness was highest on ridges, and slope and valley forest were more similar in composition with each other than they were with ridge forest. Of the fifty-two tree species encountered in the plots, nine showed a statistical affiliation to one of the three topographical positions. Main conclusions We explain patterns of forest structure and diversity in the context of chronic and catastrophic disturbances. Higher stem densities in ridge forest suggested a higher degree of disturbance on ridges, and this was supported by the fact that the height/diameter ratio of the forest was lowest on ridges, which indicated wind-cropping. We hypothesize the potential effects of topographical variation and known phenological patterns on wildlife abundances. We predict that flowering episodes of ridge-affiliated, bird-visited species (particularly Syzygium inophylloides (A. Gray) C. Muell.; Myrtaceae) will concentrate honeyeater densities on ridges, and that fruiting of the tree Canarium vitiense A. Gray (Burseraceae) could localize populations of the Pacific pigeon (Ducula pacifica). Overall (i.e. net) bat foraging patterns are unlikely to be affected by either flowering or fruiting events. Most of the tree species on Tutuila are generalist in their demographic patterns, and the island is depauperate in wildlife fauna; the evolutionary and conservation implications are discussed. We conclude with the argument that conservation of vertebrate species is essential to maintain the current generalist demographic patterns of Samoan trees.