Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group,and pairwise genome comparisons of the species of the group by means of ANI calculations

Strain BCT-7112^T was isolated in 1966 in Japan from a survey designed to obtain naturally occurring microorganisms as pure cultures in the laboratory for use as probiotics in animal nutrition. This strain, which was primarily identified as Bacillus cereus var toyoi, has been in use for more than 30 years as the active ingredient of the preparation TOYOCERIN^®, an additive for use in animal nutrition (e.g. swine, poultry, cattle, rabbits and aquaculture). Despite the fact that the strain was initially classified as B. cereus, it showed significant genomic differences from the type strains of the B. cereus group that were large enough (ANI values below 92%) to allow it to be considered as a different species within the group. The polyphasic taxonomic study presented here provides sufficient discriminative parameters to classify BCT-7112^T as a new species for which the name Bacillus toyonensis sp. nov. is proposed, with BCT-7112^T (=CECT 876^T; =NCIMB 14858^T) being designated as the type strain. In addition, a pairwise comparison between the available genomes of the whole B. cereus group by means of average nucleotide identity (ANI) calculations indicated that besides the eight classified species (including B. toyonensis), additional genomospecies could be detected, and most of them also had ANI values below 94%. ANI values were on the borderline of a species definition only in the cases of representatives of B. cereus versus B. thuringiensis, and B. mycoides and B. weihenstephanensis.     

The Evolution of the Exponent of Zipf's Law in Language Ontogeny

It is well-known that word frequencies arrange themselves according to Zipf''s law. However, little is known about the dependency of the parameters of the law and the complexity of a communication system. Many models of the evolution of language assume that the exponent of the law remains constant as the complexity of a communication systems increases. Using longitudinal studies of child language, we analysed the word rank distribution for the speech of children and adults participating in conversations. The adults typically included family members (e.g., parents) or the investigators conducting the research. Our analysis of the evolution of Zipf''s law yields two main unexpected results. First, in children the exponent of the law tends to decrease over time while this tendency is weaker in adults, thus suggesting this is not a mere mirror effect of adult speech. Second, although the exponent of the law is more stable in adults, their exponents fall below 1 which is the typical value of the exponent assumed in both children and adults. Our analysis also shows a tendency of the mean length of utterances (MLU), a simple estimate of syntactic complexity, to increase as the exponent decreases. The parallel evolution of the exponent and a simple indicator of syntactic complexity (MLU) supports the hypothesis that the exponent of Zipf''s law and linguistic complexity are inter-related. The assumption that Zipf''s law for word ranks is a power-law with a constant exponent of one in both adults and children needs to be revised.     

Nucleotide diversity of a ND5 fragment confirms that population expansion is the most suitable explanation for the mtDNA haplotype polymorphism of <Emphasis Type=Italic>Drosophila subobscura</Emphasis>

Results from mitochondria (mt) DNA restriction site analyses (RSAs) have revealed that wild populations of Drosophila subobscura are formed by two common (I and II) and some rare, often endemic, low-frequency haplotypes. In the study reported here, we analysed nucleotide diversity in a 942-bp fragment of the mtDNA ND5 gene in 48 D. subobscura individuals captured from three populations that showed haplotypes I, II or the less common ones, as well as in one additional individual belonging to D. guanche that was taken as an outgroup. RSAs and sequencing results were compared. The two approaches yielded similar nucleotide variability parameters, suggesting a consistency in the results obtained from mtDNA dynamics in natural populations of D. subobscura. Patterns of polymorphism at ND5 are most consistent with the hypothesis of population expansion after a bottleneck that may have occurred since the last glaciation or which may occur seasonally after the summer and winter. However, we cannot rule out that selection has a role in maintaining the two major haplotypes at intermediate frequencies in worldwide populations of D. subobscura.     

Life cycle assessment comparison among different reuse intensities for industrial wooden containers

Goal, scope and background  The industrial packages sector has great importance for the transport sector in Europe. These containers, mainly wooden pallets and spools, are subject to European legislation, which promotes their reuse and recycling. This study uses life cycle assessment (LCA) to assess the environmental impact of the current management system in this sector and the benefits and drawbacks of different reuse intensities as a waste prevention strategy as opposed to the recycling option. Materials and methods  In this paper, four case studies located in Spain and representative of the wooden package sector in Europe are analysed: high reuse pallet, low reuse pallet, low reuse spool and null reuse spool. For the LCA study cases, the functional unit is that required to satisfy the transport necessity of 1,000 t by road. The impact and energy consumption assessment methods used are CML 2 Baseline 2000 and Cumulative Energy Demand. Data are mostly provided by the leading enterprises and organisations in this sector. Results  The paper provides, as a first result, a comprehensive inventory of the systems under study. Secondly, our assessment shows that the systems with higher reuse intensity show a reduction in energy and wood consumption and all the environmental impact categories except for the global warming potential from 34.0% to 81.0% in the pallet study cases and from 50.4% to 72.8% in the spool ones. This reduction is at the expense of the maintenance stage, which on the contrary increases its impact, although it is still relatively small—less than 7% in all the impact categories and flow indicators of the study cases. The highest impact stages are transport, raw material extraction and the process chain. The final disposal and maintenance stages are the lowest impact, contributing at most to less than 30% of the impact in the pallet study cases and 10% in the spool cases. Discussion  Wood consumption (WC), directly related to the number of containers needed to satisfy the functional unit, is the main factor in determining the impact of the stages, especially in the raw materials extraction and process chain stages, assuming that these are undertaken with the same technologies in all the case studies. Other variables, such as the management system, the maintenance index and the final disposal scenario, affect the impact of the remaining stages: transport, maintenance and final disposal. The global warming potential results obtained demonstrate the environmental benefits of using containers made of a renewable resource such as wood instead of using other materials, but these results are not expected to prioritise the lower reuse systems because of their better performance in this category. Conclusions  Reuse, a strategy capable of reducing the environmental impacts of the wooden container systems, is preferable to recycling, while the package maintenance tasks are still feasible. Therefore, reuse, combined with recycling as final disposal, should be encouraged to reduce the demand for natural resources and the waste generated. Recommendations  Based on these results, attention should be paid to the maintenance stage, which, being the lowest-impact one, could substantially reduce the impact of the remaining stages.     

Molecular mechanisms of O-GlcNAcylation

Protein glycosylation with O-linked N-acetylglucosamine (O-GlcNAc) is a reversible post-translational modification of serines/threonines on metazoan proteins and occurring with similar time scales, dynamics and stoichiometry as protein phosphorylation. Levels of this modification are regulated by two enzymes-O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (OGA). Although the biochemistry of these enzymes and functional implications of O-GlcNAc have been studied extensively, until recently the structures and molecular mechanisms of OGT/OGA were not understood. This review covers a body of recent work that has led to an understanding of the structure of OGA, its catalytic mechanism and the development of a plethora of different inhibitors that are finding their use in cell biological studies towards the functional implications of O-GlcNAc. Furthermore, the very recent structure determination of a bacterial OGT orthologue has given the first insights into the contribution of the tetratricopeptide repeats (TPRs) to the active site and the role of some residues in catalysis and substrate binding.