The effect of tRNA levels on decoding times of mRNA codons

The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (−0.38 to −0.66, all P values <0.006); in addition, we show that when considering tRNA concentrations, codons decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool.     

Localisation of RFLPs of the medium chain acyl-CoA dehydrogenase gene

Summary Six restriction fragment length polymorphisms (RFLPs) of the gene are described. Three of these are in linkage disequilibrium. Hybridisation with sub-probes allowed localisation of the RFLPs to different regions of the gene.     

Functional analysis of phosphorylation of the mitotic centromere-associated kinesin by Aurora B kinase in human tumor cells

Mitotic centromere-associated kinesin (MCAK) is the best characterized member of the kinesin-13 family and plays important roles in microtubule dynamics during mitosis. Its activity and subcellular localization is tightly regulated by an orchestra of mitotic kinases, such as Aurora B. It is well known that serine 196 of MCAK is the major phosphorylation site of Aurora B in Xenopus leavis extracts and that this phosphorylation regulates its catalytic activity and subcellular localization. In the current study, we have addressed the conserved phosphorylation site serine 192 in human MCAK to characterize its function in more depth in human cancer cells. Our data confirm that S192 is the major phosphorylation site of Aurora B in human MCAK and that this phosphorylation has crucial roles in regulating its catalytic activity and localization at the kinetochore/centromere region in mitosis. Interfering with this phosphorylation leads to a delayed progression through prometa- and metaphase associated with mitotic defects in chromosome alignment and segregation. We show further that MCAK is involved in directional migration and invasion of tumor cells, and interestingly, interference with the S192 phosphorylation affects this capability of MCAK. These data provide the first molecular explanation for clinical observation, where an overexpression of MCAK was associated with lymphatic invasion and lymph node metastasis in gastric and colorectal cancer patients.     

Selection of the conodont Idiognathodus simulator (Ellison) as the event marker for the base of the global Gzhelian Stage (Upper Pennsylvanian, Carboniferous)

Studies carried out for more than 10 years by the Task Group to establish GSSPs at the base of the Moscovian–Kasimovian and Kasimovian–Gzhelian boundaries have resulted in the proposal that the level at which the conodont species Idiognathodus simulator (Ellison, 1941) first appears be selected to mark the base of the Gzhelian Stage. This expands this eastern European chronostratigraphic unit to a global scale.I. simulator (sensu Barrick et al., 2008) has been identified so far in Midcontinent and eastern North America, the Moscow and Donets basins and southern Urals of eastern Europe, and in south-central China. Correlation of this level based on this species and other conodont species can be reinforced in some areas by ammonoid and fusulinid data.     

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

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Variability,function and phylogenetic significance of periostracal microprojections in unionoid bivalves (Mollusca)

Microprojections of unionoid shells are virtually unstudied but could be important characters for resolving questions on the phylogeny and ecology of these bivalves. By investigating 26 unionoid and three species of their closest living relatives, the Trigonioida, using scanning electron microscopy, we identified three types of periostracal microprojections. (1) Microridges were present only in one species from each of the two unionoid families Mycetopodidae (Anodontites trapesialis) and Iridinidae (Chambardia bourguignati) and may represent a synapomorphy for the mycetopodid‐iridinid clade. In A. trapesialis, microridges were additionally equipped with (2)ensp;flag‐like projections (microfringes), possibly a synapomorphic character for the Mycetopodidae. Examination of partially bleached specimens indicated that both microridges and microfringes are predominantly or purely organic. In contrast, previously undescribed (3) spicule‐like spikes represent calcifications within the periostracum. These were found in 20 of the 29 species and four of the six unionoid families. Spikes were particularly large and abundant in umbonal (juvenile) shell regions and species characteristic of fast‐flowing habitats. These structures may thus serve in protecting the periostracum and shell underneath, and/or stabilizing life position by increasing shell friction. Microfringes and microridges, on the other hand, possibly aid in the orientation of the mussel within the sediment.     

Germination responses of three grassland species differ between native and invasive origins

The germination stage is critical in plant life-history and is also a key process during the expansion of species’ ranges into new environments. In this study we investigated the germination patterns of three plant species (Achillea millefolium, Hieracium pilosella and Hypericum perforatum) that are invasive to New Zealand (NZ) and native to Central Europe. We asked whether the species show differences in germination temperature requirements, germination speed and maximum germination rates, and thus, whether they display evidence of adaptation to different conditions in the invasive range. Seeds from three populations per species and region were subjected to three different temperature regimes to compare germination rates among origins and across temperature conditions. For Achillea millefolium and Hypericum perforatum, germination rates were significantly higher for invasive NZ provenances than for native German ones. Seeds from invasive populations of all three species displayed increased maximum germination at medium temperature conditions when compared to native populations, which indicates altered germination strategies in the invaded range. Changes in temporal development patterns were most conspicuous for invasive Hieracium pilosella and Hypericum perforatum populations. These findings imply that adaptation in germination patterns towards different climatic conditions in invasive populations has occurred. Our study emphasises the importance of the germination stage during plant invasion and its role in explaining range expansion of these species.     

FT-IR Spectroscopy for Rapid Differentiation of Aspergillus flavus, Aspergillus fumigatus, Aspergillus parasiticus and Characterization of Aflatoxigenic Isolates Collected from Agricultural Environments

In agricultural areas, Aspergillus flavus, Aspergillus fumigatus and Aspergillus parasiticus are commonly identified in various feedstuffs and bioaerosols originated from feed handling. Some isolates belonging to these fungal species could produce mycotoxins and constitute a risk factor for human and animal health. In this study, Fourier-transform infrared spectroscopy was used for a rapid detection and characterization of 99 isolates collected from agricultural areas. The results showed a first cluster corresponding to strains previously attributed to the A. fumigatus group according to current taxonomic concepts, and a second cluster divided in 2 groups around reference strains of A. flavus and A. parasiticus species. The toxigenic capacity of isolates was evaluated by high performance liquid chromatography coupled to mass spectrometry. In the A. flavus group, only 6 strains of A. parasiticus and 4 strains of A. flavus were able to produce aflatoxins on culture media. FT-IR spectroscopy, respectively, allowed the differentiation of non-toxigenic and toxigenic A. flavus and A. parasiticus isolates at 75 and 100%. Discrimination between toxigenic and non-toxigenic A. fumigatus was not possible because all of the isolates produced at least one mycotoxin.