The Role of Peripheral Myelin Protein 2 in Remyelination

The protein component of the myelin layer is essential for all aspects of peripheral nerves, and its deficiency can lead to structural and functional impairment. The presence of peripheral myelin protein 2 (P2, PMP2, FABP8, M-FABP) in Schwann cells has been known for decades and shown recently to be involved in the lipid homeostasis in the peripheral neural system. However, its precise role during de- and remyelination has yet to be elucidated. To this end, we assessed remyelination after sciatic nerve crush injury in vivo, and in an experimental de/remyelination ex vivo myelinating culture model in P2-deficient (P2 ^?/? ) and wild-type (WT) animals. In vivo, the nerve crush paradigm revealed temporal structural and functional changes in P2 ^?/? mice as compared to WT animals. Concomitantly, P2 ^?/? DRG cultures demonstrated the presence of shorter internodes and enlarged nodes after ex vivo de/remyelination. Together, these data indicate that P2 may play a role in remyelination of the injured peripheral nervous system, presumably by affecting the nodal and internodal configuration.     

Coordinate systems for supergenomes

Background

Genome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting comparative, evolutionary analysis is also growing. In particular, efficient tools to visualize-omics data simultaneously for multiple species are sorely lacking. A first and crucial step in this direction is the construction of a common coordinate system. Since genomes not only differ by rearrangements but also by large insertions, deletions, and duplications, the use of a single reference genome is insufficient, in particular when the number of species becomes large.

Results

The computational problem then becomes to determine an order and orientations of optimal local alignments that are as co-linear as possible with all the genome sequences. We first review the most prominent approaches to model the problem formally and then proceed to showing that it can be phrased as a particular variant of the Betweenness Problem. It is NP hard in general. As exact solutions are beyond reach for the problem sizes of practical interest, we introduce a collection of heuristic simplifiers to resolve ordering conflicts.

Conclusion

Benchmarks on real-life data ranging from bacterial to fly genomes demonstrate the feasibility of computing good common coordinate systems.

     

Superbubbles revisited

Background

Superbubbles are distinctive subgraphs in direct graphs that play an important role in assembly algorithms for high-throughput sequencing (HTS) data. Their practical importance derives from the fact they are connected to their host graph by a single entrance and a single exit vertex, thus allowing them to be handled independently. Efficient algorithms for the enumeration of superbubbles are therefore of important for the processing of HTS data. Superbubbles can be identified within the strongly connected components of the input digraph after transforming them into directed acyclic graphs. The algorithm by Sung et al. (IEEE ACM Trans Comput Biol Bioinform 12:770–777, 2015) achieves this task in \(\mathcal {O}(m~log(m))\)-time. The extraction of superbubbles from the transformed components was later improved to by Brankovic et al. (Theor Comput Sci 609:374–383, 2016) resulting in an overall \(\mathcal {O}(m+n)\)-time algorithm.

Results

A re-analysis of the mathematical structure of superbubbles showed that the construction of auxiliary DAGs from the strongly connected components in the work of Sung et al. missed some details that can lead to the reporting of false positive superbubbles. We propose an alternative, even simpler auxiliary graph that solved the problem and retains the linear running time for general digraph. Furthermore, we describe a simpler, space-efficient \(\mathcal {O}(m+n)\)-time algorithm for detecting superbubbles in DAGs that uses only simple data structures.

Implementation

We present a reference implementation of the algorithm that accepts many commonly used formats for the input graph and provides convenient access to the improved algorithm. https://github.com/Fabianexe/Superbubble.

     

The interaction between vitamin D receptor polymorphisms and sun exposure around time of diagnosis influences melanoma survival

Evidence on the relationship between the vitamin D pathway and outcomes in melanoma is growing, although it is not always clear. We investigated the impact of measured levels of sun exposure at diagnosis on associations of vitamin D receptor gene (VDR) polymorphisms and melanoma death in 3336 incident primary melanoma cases. Interactions between six SNPs and a common 3′‐end haplotype were significant (p < .05). These SNPs, and a haplotype, had a statistically significant association with survival among subjects exposed to high UVB in multivariable regression models and exerted their effect in the opposite direction among those with low UVB. SNPs rs1544410/BsmI and rs731236/TaqI remained significant after adjustment for multiple testing. These results suggest that the association between VDR and melanoma‐specific survival is modified by sun exposure around diagnosis, and require validation in an independent study. Whether the observed effects are dependent or independent of vitamin D activation remains to be determined.     

Optimization of Component Yields and Thermal Properties by Organosolv Fractionation of Loblolly Pine (<Emphasis Type="Italic">Pinus taeda</Emphasis>) Using Response Surface Design

Lignin, a low value by-product of biomass fractionation, is of current particular interest for the production of value added materials such as carbon fibers within a biorefinery. Accordingly, we have isolated lignin, hemicellulose, and cellulose by organosolv fractionation of loblolly pine (Pinus taeda) under the influence different fractionation severities (2.50–3.31). A designed experimental matrix targeted maximum lignin and pulp yields and lignin glass transition temperature (T_g) as a function of several process parameters. Optimal fractionation conditions were estimated from an enhanced regression model of the statistically significant variables generated using response surface design (RSD). The most significant factor influencing lignin and pulp yields was solvent composition (p-value <?0.0001). A maximum lignin yield of 94.71 wt% and maximum cellulose yield of 74.96 wt% were determined at combined severities of 3.21 and 2.63, respectively. The lowest T_g of 132.83 °C was found at a combined severity of 2.82.     

The use of enhanced polymer one-step staining reagents for immunoenzyme double-labelling

Summary The newly developed peroxidase-labelled Enhanced Polymer One-Step (EPOS) reagents were applied, together with an unlabelled primary mouse antibody, in a multistep double-labelling protocol. Enzyme label reporter combinations consisted of either peroxidase and alkaline phosphatase in red and blue, respectively, or β-galactosidase and alkaline phosphatase in turquoise and red, respectively. The latter enzyme combination was introduced using a rabbit antiperoxidase antibody and an enzyme-labelled anti-rabbit immunoglobulin antibody. The multistep procedure was tested using five different antibody combinations on cryostat and Carnoy- or formalin-fixed, paraffin-embedded sections. In each instance, clear and distinct labelling was obtained, either with the two antigens at separate sites, or with an overlap in distribution. In the latter situation, the sites of co-localization were marked by mixed colours, which were distinct and readily discriminated from the two basic colours.     

The influence of a dissolved inorganic nitrogen gradient on phytoplankton community dynamics in a chain of lakes

In a chain of lakes along which nutrient availability varies in a gradient, we performed factorial nutrient enrichment experiments to determine if nitrogen limitation was the principal factor controlling the differences in phytoplankton biomass, photosynthetic productivity, diversity, and species composition among two of the lakes in the chain. In the least productive lake, East Graham Lake, P and C enrichments (in the absence of N enrichment) had no effect on biomass and diversity, whereas within two weeks the N enrichments (alone or in any combination with P and/or C) increased the biomass and decreased the diversity of East Graham Lake phytoplankton to levels similar or identical to those in more productive Shoe Lake. Short-term ¹⁴C photosynthetic rates in East Graham Lake water also responded only to N in the third week. However, photosynthesis was stimulated by P in the first week, and a few species did increase in numbers with P enrichment, suggesting that some degree of P limitation remains in addition to the strong N limitation in East Graham Lake. A number of species responded individually to the enrichments in a manner similar to that of the overall community, and a strong overlapping of discriminant analysis scores for N-enriched East Graham Lake with those of Shoe Lake was consistent with our prediction that the community structure of N-enriched East Graham Lake water would shift toward that of Shoe Lake. However, many species did not respond consistently with these results, and the nutrients tested were clearly not a major factor in the differences in abundance of those species among the two lakes. The results support the argument that overall biomass production and diversity of the phytoplankton community in a lake can be a relatively simple function of a single most-limiting nutrient. However, many of the species responses also confirm that, while nutrient availability is an important factor in the control of the species composition of the community, other factors are likely to prevent reliable predictions of all species effects on the basis of nutrient availability alone.     

Four different head shapes in Daphnia hyalina (Leydig) induced by the presence of larvae of Chaoborus flavicans (Meigen)

In many species of Daphnia spines, neck teeth, and enlarged or reshaped helmets are well-known as defences against invertebrate predators. Until now, Daphnia hyalina (Leydig, 1860), a common species in many European lakes, has appeared to be an exception to this rule.Here, we provide evidence that the larvae of Chaoborus flavicans (Meigen) also can induce morphological changes in D. hyalina. Specimens react morphologically to the presence of larvae in three ways: (a) by changes in the shape of head shield, (b) by the formation of spine(s) on the head, and (c) by the elongation of the tail spine. The frequency and intensity of these morphological changes are correlated positively with midge larvae densities. The most pronounced reactions occurred in young D. hyalina.The predator kairomone also induced changes in Daphnia body size.     

Recombinant Hansenula polymorpha as a biocatalyst: coexpression of the spinach glycolate oxidase (GO) and the S. cerevisiae catalase T (CTT1) gene

 The methylotrophic yeast Hansenula polymorpha has been developed as an efficient production system for heterologous proteins. The system offers the possibility to cointegrate heterologous genes in anticipated fixed copy numbers into the chromosome. As a consequence coproduction of different proteins in stoichiometric ratios can be envisaged. This provides options to design this yeast as an industrial biocatalyst in procedures where several enzymes are required for the efficient conversion of a given inexpensive compound into a valuable product. To this end recombinant strains have been engineered with multiple copies of expression cassettes containing the glycolate oxidase (GO) gene from spinach and the catalase T (CTT1) gene from S. cerevisiae. The newly created strains produce high levels of the peroxisomal glycolate oxidase and the cytosolic catalase T. The strains efficiently convert glycolate into glyoxylic acid, oxidizing the added substrate and decomposing the peroxide formed during this reaction into water and oxygen. Received: 31 October 1995/Received last revision: 23 February 1996/Accepted: 4 March 1996