The osteology of the golden grey mullet Liza aurata (Teleostei: Mugiliformes: Mugilidae) including interactive three-dimensional reconstructions

Grey mullets are remarkably characterized by their overall uniform external morphology. Identifying species as well as positioning the Mugiliformes in a phylogenetic context is rather difficult. Most recently they were placed in the newly erected Ovalentaria, but more detailed relationships to potential sister taxa were not resolved. Studying the internal morphology, especially the osteology, might provide new insights into the evolution of the Mugiliformes as well as help clarify their phylogenetic position within the Ovalentaria. A detailed osteology of the golden grey mullet Liza aurata is presented. The use of cleared and stained specimens allowed for a complete examination of bony and cartilaginous structures, and a 3D reconstruction from a μCT data set provided additional information on the positional relationships of the bones. Following this, the data obtained were compared with different mugilid species, particularly with the flathead grey mullet Mugil cephalus. Several differences between these species could be identified, such as the position of the basisphenoid, the shape of the hyomandibular and the composition of the branchial arches. These characters might help in understanding the evolutionary changes happening within the mugiliforms and will provide the basis to study this taxon in detail, finally allowing the reconstruction of the body plan of grey mullets.     

Season of Birth and Lung Fibrosis among Workers Exposed to Asbestos

The season of birth has been suggested to influence the development of some diseases, but its role in lung fibrosis seems to not have been studied previously. The aim of this study was to investigate the relation between the season of birth and fibrotic abnormalities as detected radiologically in high‐resolution computed tomography (HRCT) among workers exposed to asbestos. The HRCT examination was performed on 528 study subjects. Multiple ordinal regression analysis adjusting for covariates was used to study the relations between birth month or season and radiological fibrosis signs. Subjects born in autumn or winter had more extensive fibrotic changes than those born in spring or summer. This applied to all fibrotic changes, apart from subpleural nodules, but only the overall fibrosis score, septal lines, and honeycombing showed statistically significantly higher values in comparison to spring births. The highest scores were detected among those born in autumn and winter months (September–February). These results suggest that there are differences in fibrotic radiological abnormalities according to the season of birth in adults exposed to asbestos. Several hypotheses could explain the observed findings, including the effects of early respiratory infections, cold temperature, and differences in air pollution levels, as well as some metabolic and hormonal effects.     

Root growth in biopores—evaluation with in situ endoscopy

Background and aims

The significance of biopores for nutrient acquisition from the subsoil depends on root-soil contact, which in turn is influenced by root architecture. The aim of this study was to detect differences regarding the architecture and root-soil contact of homorhizous barley roots (Hordeum vulgare L.) and allorhizous oilseed rape roots (Brassica napus L.) growing in biopores.

Methods

In situ endoscopy was used as a technique that allows non-destructive display of pore wall characteristics and root morphology inside large biopores under field conditions.

Results

For both crops, about 85 % of all roots did establish contact to the pore wall. However, according to their different root architecture, the two crops varied in their strategy of resource acquisition: While barley was characterized by thin vertical or ingrowing roots, most of them in direct contact to the pore wall, oilseed rape established contact to the pore wall predominantly via lateral roots.

Conclusions

Root morphological and pore wall assessment with in situ endoscopy in combination with detailed studies of soil biochemical and soil physical parameters of the pore wall is considered an essential prerequisite for more precise future modelling of nutrient acquisition and uptake.     

Genetic characterisation and heterologous expression of leucocin C, a class IIa bacteriocin from Leuconostoc carnosum 4010

Leuconostoc carnosum 4010 is a protective culture for meat products. It kills the foodborne pathogen Listeria monocytogenes by producing two class IIa (pediocin-like) bacteriocins, leucocin A and leucocin C. The genes for leucocin A production have previously been characterised from Leuconostoc gelidum UAL 187, whereas no genetic studies about leucocin C has been published. Here, we characterised the genes for the production of leucocins A and C in L. carnosum 4010. In this strain, leucocin A and leucocin C operons were localised in different plasmids. Unlike in L. gelidum, leucocin A operon in L. carnosum 4010 only contained the structural and the immunity genes lcaAB without transporter genes lcaECD. On the contrary, leucocin C cluster included two intact operons. Novel genes lecCI encode the leucocin C precursor and the 97-aa immunity protein LecI, respectively. LecI shares 48 % homology with the immunity proteins of sakacin P and listeriocin. Another leucocin C operon lecXTS, encoding an ABC transporter and an accessory protein, was 97 % identical with the leucocin A transporter operon lcaECD of L. gelidum. For heterologous expression of leucocin C in Lactococcus lactis, the mature part of the lecC gene was fused with the signal sequence of usp45 in the secretion vector pLEB690. L. lactis secreted leucocin C efficiently, as shown by large halos on lawns of L. monocytogenes and Leuconostoc mesenteroides indicators. The function of LecI was then demonstrated by expressing the gene lecI in L. monocytogenes. LecI-producing Listeria was less sensitive to leucocin C than the vector strain, thus corroborating the immunity function of LecI.     

A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Background

Recently, Marcus et al. (Bioinformatics 30:3476–83, 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an \(O(n\log g)\) time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where n is the total length of the genomes and g is the length of the longest genome. Baier et al. (Bioinformatics 32:497–504, 2016) improved their result.

Results

In this paper, we propose a new space-efficient representation of the compressed de Bruijn graph that adds the possibility to search for a pattern (e.g. an allele—a variant form of a gene) within the pan-genome. The ability to search within the pan-genome graph is of utmost importance and is a design goal of pan-genome data structures.

     

Phenotypic plasticity in growth and fecundity induced by strong population fluctuations affects reproductive traits of female fish

Fish are known for their high phenotypic plasticity in life‐history traits in relation to environmental variability, and this is particularly pronounced among salmonids in the Northern Hemisphere. Resource limitation leads to trade‐offs in phenotypic plasticity between life‐history traits related to the reproduction, growth, and survival of individual fish, which have consequences for the age and size distributions of populations, as well as their dynamics and productivity. We studied the effect of plasticity in growth and fecundity of vendace females on their reproductive traits using a series of long‐term incubation experiments. The wild parental fish originated from four separate populations with markedly different densities, and hence naturally induced differences in their growth and fecundity. The energy allocation to somatic tissues and eggs prior to spawning served as a proxy for total resource availability to individual females, and its effects on offspring survival and growth were analyzed. Vendace females allocated a rather constant proportion of available energy to eggs (per body mass) despite different growth patterns depending on the total resources in the different lakes; investment into eggs thus dictated the share remaining for growth. The energy allocation to eggs per mass was higher in young than in old spawners and the egg size and the relative fecundity differed between them: Young females produced more and smaller eggs and larvae than old spawners. In contrast to earlier observations of salmonids, a shortage of maternal food resources did not increase offspring size and survival. Vendace females in sparse populations with ample resources and high growth produced larger eggs and larvae. Vendace accommodate strong population fluctuations by their high plasticity in growth and fecundity, which affect their offspring size and consequently their recruitment and productivity, and account for their persistence and resilience in the face of high fishing mortality.     

Sphingosine-1-Phosphate Lyase Deficient Cells as a Tool to Study Protein Lipid Interactions

Cell membranes contain hundreds to thousands of individual lipid species that are of structural importance but also specifically interact with proteins. Due to their highly controlled synthesis and role in signaling events sphingolipids are an intensely studied class of lipids. In order to investigate their metabolism and to study proteins interacting with sphingolipids, metabolic labeling based on photoactivatable sphingoid bases is the most straightforward approach. In order to monitor protein-lipid-crosslink products, sphingosine derivatives containing a reporter moiety, such as a radiolabel or a clickable group, are used. In normal cells, degradation of sphingoid bases via action of the checkpoint enzyme sphingosine-1-phosphate lyase occurs at position C2-C3 of the sphingoid base and channels the resulting hexadecenal into the glycerolipid biosynthesis pathway. In case the functionalized sphingosine looses the reporter moiety during its degradation, specificity towards sphingolipid labeling is maintained. In case degradation of a sphingosine derivative does not remove either the photoactivatable or reporter group from the resulting hexadecenal, specificity towards sphingolipid labeling can be achieved by blocking sphingosine-1-phosphate lyase activity and thus preventing sphingosine derivatives to be channeled into the sphingolipid-to-glycerolipid metabolic pathway. Here we report an approach using clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated nuclease Cas9 to create a sphingosine-1-phosphate lyase (SGPL1) HeLa knockout cell line to disrupt the sphingolipid-to-glycerolipid metabolic pathway. We found that the lipid and protein compositions as well as sphingolipid metabolism of SGPL1 knock-out HeLa cells only show little adaptations, which validates these cells as model systems to study transient protein-sphingolipid interactions.     

All-Cause and Cause-Specific Mortality among Users of Basal Insulins NPH,Detemir, and Glargine

Background

Insulin therapy in type 2 diabetes may increase mortality and cancer incidence, but the impact of different types of basal insulins on these endpoints is unclear. Compared to the traditional NPH insulin, the newer, longer-acting insulin analogues detemir and glargine have shown benefits in randomized controlled trials. Whether these advantages translate into lower mortality among users in real life is unknown.

Objective

To estimate the differences in all-cause and cause-specific mortality rates between new users of basal insulins in a population-based study in Finland.

Methods

23 751 individuals aged ≥40 with type 2 diabetes, who initiated basal insulin therapy in 2006–2009 were identified from national registers, with comprehensive data for mortality, causes of death, and background variables. Propensity score matching was performed on characteristics. Follow-up time was up to 4 years (median 1.7 years).

Results

2078 deaths incurred. With NPH as reference, the adjusted HRs for all-cause mortality were 0.39 (95% CI, 0.30–0.50) for detemir, and 0.55 (95% CI, 0.44–0.69) for glargine. As compared to glargine, the HR was 0.71 (95% CI, 0.54–0.93) among detemir users. Compared to NPH, the mortality risk for both cardiovascular causes as well as cancer were also significantly lower for glargine, and especially for detemir in adjusted analysis. Furthermore, the results were robust in various sensitivity analyses.

Conclusion

In real clinical practice, mortality was substantially higher among users of NPH insulin as compared to insulins detemir or glargine. Considering the large number of patients who require insulin therapy, this difference in risk may have major clinical and public health implications. Due to limitations of the observational study design, further investigation using an interventional study design is warranted.