The sensitivity of Afromontane tarns in the Maloti-Drakensberg region of South Africa and Lesotho to acidic deposition

Despite their remoteness from sources of atmospheric pollutant emissions, the Afromontane tarns in the Maloti-Drakensberg region are perfect candidates to study the negative effects of acidifying atmospheric pollution, because mountain lakes are widely recognised as sentinel ecosystems, unimpacted by direct human disturbance within their catchments. Thirty-four tarns were sampled in the Maloti-Drakensberg region and most were found to be extremely sensitive to acidic deposition, as indicated by their low acid neutralising capacity. There are very few studies of freshwater critical loads for any region within South Africa. The steady-state water chemistry model (SSWC) was adapted and used to determine critical loads, whereas exceedance was estimated relative to modelled regional deposition data, in order to understand the risk of harmful effects to aquatic ecosystems. Seventy-six percent of sampled sites across the Maloti-Drakensberg would exceed critical loads even at the lowest modelled deposition levels, but there are no current measured deposition data for the region. The sensitivity of the Maloti-Drakensberg tarns needs to be considered in future policy formulation regarding acceptable levels of acidifying atmospheric pollution from South Africa’s energy sector and indicates the need for assessing aquatic ecosystem impacts in other regions of South Africa.     

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

Partial Least Squares-Discriminant Analysis (PLS-DA) is a PLS regression method with a special binary ‘dummy’ y-variable and it is commonly used for classification purposes and biomarker selection in metabolomics studies. Several statistical approaches are currently in use to validate outcomes of PLS-DA analyses e.g. double cross validation procedures or permutation testing. However, there is a great inconsistency in the optimization and the assessment of performance of PLS-DA models due to many different diagnostic statistics currently employed in metabolomics data analyses. In this paper, properties of four diagnostic statistics of PLS-DA, namely the number of misclassifications (NMC), the Area Under the Receiver Operating Characteristic (AUROC), Q ² and Discriminant Q ² (DQ ²) are discussed. All four diagnostic statistics are used in the optimization and the performance assessment of PLS-DA models of three different-size metabolomics data sets obtained with two different types of analytical platforms and with different levels of known differences between two groups: control and case groups. Statistical significance of obtained PLS-DA models was evaluated with permutation testing. PLS-DA models obtained with NMC and AUROC are more powerful in detecting very small differences between groups than models obtained with Q ² and Discriminant Q ² (DQ ²). Reproducibility of obtained PLS-DA models outcomes, models complexity and permutation test distributions are also investigated to explain this phenomenon. DQ ² and Q ² (in contrary to NMC and AUROC) prefer PLS-DA models with lower complexity and require higher number of permutation tests and submodels to accurately estimate statistical significance of the model performance. NMC and AUROC seem more efficient and more reliable diagnostic statistics and should be recommended in two group discrimination metabolomic studies.

     

Characteristics of hollows and hollow‐bearing trees in semi‐arid river red gum woodland and potential limitations for hollow‐dependent wildlife

Up to 37 species of the birds and microbats inhabiting inland Australia are dependent on tree cavities for breeding or roosting. The river red gum (Eucalyptus camaldulensis), a well‐known hollow‐bearing tree species, occurs in linear semi‐arid woodland along thousands of kilometres of ephemeral river channels and is the only tree species that provides widespread, aggregated hollow resources across a landscape otherwise dominated by shrublands. Here we assess the type and quantity of hollows available along ephemeral rivers of the MacDonnell Ranges bioregion in central Australia and determine which characteristics of river red gums best predict the abundance and characteristics of different tree hollows, as first steps towards assessing the current availability of hollows in the region. Approximately a third of all river red gums sampled were hollow‐bearing, but individual trees with abundant hollows were rare. Further, 36% of hollows had an entrance ≤ 5 cm, and 37% had entrances which were 6–10 cm in diameter, whereas only 13% of hollows had an entrance diameter > 20 cm suitable for larger hollow‐using species. Large and high hollows only occurred on trees that did not display post‐disturbance resprouting. Trees with multiple and diverse hollows were rare and tended to be in advanced stages of senescence and had larger stems (82.3 ± 3.33 cm) and were taller (14.4 ± 0.53 m) compared to non‐hollow‐bearing trees (23.44 ± 1.68 cm, 8.0 ± 0.34 m). Further research is required to establish whether the current abundance of hollows and diversity of hollow types are limiting to cavity‐dependent wildlife, and to identify any threats to availability of hollows.     

Differences in the carbon tetrachloride-induced damage to components of the smooth and rough endoplasmic reticulum from rat liver

There is a higher activity of ethyl morphine N-demethylase (EM-ase) and cytochrome P-450 (P-450) reductase as well as higher P-450 content in the smooth endoplasmic reticulum (SER) than in the rough endoplasmic reticulum (RER). The extent of the irreversible binding of the¹⁴C from¹⁴CCl₄ to lipids and proteins, as well as the CCl₄-induced destruction of P-450 is more intense in SER than in RER while the opposite was found for glucose 6-phosphatase (G6P-ase) destruction. CCl₄-induced lipid peroxidation is as intense in SER as is in RER.¹⁴C from¹⁴CCl₄ gets irreversibly bound to ribosomal proteins.     

Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida

Background

The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure – the syncytium – which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium.

Results

The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure.

Conclusion

This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-923) contains supplementary material, which is available to authorized users.     

High yield expression of leptospirosis vaccine candidates LigA and LipL32 in the methylotrophic yeast <Emphasis Type="Italic">Pichia pastoris</Emphasis>

Background  

Leptospirosis, a zoonosis caused by Leptospira spp., is recognized as an emergent infectious disease. Due to the lack of adequate diagnostic tools, vaccines are an attractive intervention strategy. Recombinant proteins produced in Escherichia coli have demonstrated promising results, albeit with variable efficacy. Pichia pastoris is an alternative host with several advantages for the production of recombinant proteins.     

Dynamic metabolomic data analysis: a tutorial review

In metabolomics, time-resolved, dynamic or temporal data is more and more collected. The number of methods to analyze such data, however, is very limited and in most cases the dynamic nature of the data is not even taken into account. This paper reviews current methods in use for analyzing dynamic metabolomic data. Moreover, some methods from other fields of science that may be of use to analyze such dynamic metabolomics data are described in some detail. The methods are put in a general framework after providing a formal definition on what constitutes a ‘dynamic’ method. Some of the methods are illustrated with real-life metabolomics examples.     

Sowing density and harvest time affect fibre content in hemp (Cannabis sativa) through their effects on stem weight

Sowing density and harvest time are considered important crop management factors influencing fibre quantity and quality in hemp (Cannabis sativa). We investigated whether the effects of these factors are essentially different or that both factors affect stem weight and thereby total and long‐fibre content. The effects of all combinations of three sowing densities and three harvest times were studied for six different stem parts. Almost 500 samples consisting of stem parts from 50 plants and with a length of 50 cm were tested. Fibres were extracted by a controlled warm‐water retting procedure, followed by breaking and scutching. The initial sample weight was fractionated into retting losses, wood, tow and long fibre. In both Italy and the Netherlands, crops were successfully established with different stem densities (99–283 m^?2), plant heights (146–211 cm) and stem diameters (4.5–8.4 mm) at harvest. Stem dry matter yields (6.8–11.7 Mg ha^?1) increased with a delay in harvest time but were not affected by sowing density. Retting loss percentages were lower in lower stem parts and decreased with later harvest because maturation was associated with increasing amounts of fibre and wood. Within a certain stem part, however, the absolute retting losses were constant with harvest time. Multiple linear regression analyses showed that the amount of fibre in a hemp stem is almost completely determined by the weight and the position of that stem part. When the plant grows, the increase in dry matter is split up into fibres and wood in a fixed way. This total fibre/wood ratio was highest in the middle part of the stem and lower towards both bottom and top. Sowing density and harvest time effects were indirect through stem weight. The long‐fibre weight per stem increased with the total fibre weight and hence with stem weight. Stem weight increased with harvest time; as harvest time did not affect plant density, the highest long‐fibre yields were obtained at the last harvest time. The long fibre/total fibre ratio was lowest in the bottom 5 cm of the stems but similar for all other parts. Sowing density and harvest time effects again were indirect. Fibre percentages in retted hemp decreased with increasing stem weights towards a level that is presumably a variety characteristic. The dry matter increase between harvests, however, is much more important with respect to total and long‐fibre yield.     

Gene expression profiling of early intervertebral disc degeneration reveals a down-regulation of canonical Wnt signaling and caveolin-1 expression: implications for development of regenerative strategies

Introduction

Early degeneration of the intervertebral disc (IVD) involves a change in cellular differentiation from notochordal cells (NCs) in the nucleus pulposus (NP) to chondrocyte-like cells (CLCs). The purpose of this study was to investigate the gene expression profiles involved in this process using NP tissue from non-chondrodystrophic and chondrodystrophic dogs, a species with naturally occurring IVD degeneration.

Methods

Dual channel DNA microarrays were used to compare 1) healthy NP tissue containing only NCs (NC-rich), 2) NP tissue with a mixed population of NCs and CLCs (Mixed), and 3) NP tissue containing solely CLCs (CLC-rich) in both non-chondrodystrophic and chondrodystrophic dogs. Based on previous reports and the findings of the microarray analyses, canonical Wnt signaling was further evaluated using qPCR of relevant Wnt target genes. We hypothesized that caveolin-1, a regulator of Wnt signaling that showed significant changes in gene expression in the microarray analyses, played a significant role in early IVD degeneration. Caveolin-1 expression was investigated in IVD tissue sections and in cultured NCs. To investigate the significance of Caveolin-1 in IVD health and degeneration, the NP of 3-month-old Caveolin-1 knock-out mice was histopathologically evaluated and compared with the NP of wild-type mice of the same age.

Results

Early IVD degeneration involved significant changes in numerous pathways, including Wnt/β-catenin signaling. With regard to Wnt/β-catenin signaling, axin2 gene expression was significantly higher in chondrodystrophic dogs compared with non-chondrodystrophic dogs. IVD degeneration involved significant down-regulation of axin2 gene expression. IVD degeneration involved significant down-regulation in Caveolin-1 gene and protein expression. NCs showed abundant caveolin-1 expression in vivo and in vitro, whereas CLCs did not. The NP of wild-type mice was rich in viable NCs, whereas the NP of Caveolin-1 knock-out mice contained chondroid-like matrix with mainly apoptotic, small, rounded cells.

Conclusions

Early IVD degeneration involves down-regulation of canonical Wnt signaling and Caveolin-1 expression, which appears to be essential to the physiology and preservation of NCs. Therefore, Caveolin-1 may be regarded an exciting target for developing strategies for IVD regeneration.