Insertion of leader peptidase into the thylakoid membrane during synthesis in a chloroplast translation system

The mechanisms of targeting and insertion of chloroplast-encoded thylakoid membrane proteins are poorly understood. In this study, we have used a translation system isolated from chloroplasts to begin to investigate these mechanisms. The bacterial membrane protein leader peptidase (Lep) was used as a model protein because its targeting and insertion mechanisms are well understood for Escherichia coli and for the endoplasmic reticulum. Lep could thus provide insight into the functional homologies between the different membrane systems. Lep was efficiently expressed in the chloroplast translation system, and the protein could be inserted into thylakoid membranes with the same topology as in E. coli cytoplasmic membranes, following the positive-inside rule. Insertion of Lep into the thylakoid membrane was stimulated by the trans-thylakoid proton gradient and was strongly inhibited by azide, suggesting a requirement for SecA activity. Insertion most likely occurred in a cotranslational manner, because insertion could only be observed if thylakoid membranes were present during translation reactions but not when thylakoid membranes were added after translation reactions were terminated. To halt the elongation process at different stages, we translated truncated Lep mRNAs without a stop codon, resulting in the formation of stable ribosome nascent chain complexes. These complexes showed a strong, salt-resistant affinity for the thylakoid membrane, implying a functional interaction of the ribosome with the membrane and supporting a cotranslational insertion mechanism for Lep. Our study supports a functional homology for the insertion of Lep into the thylakoid membrane and the E. coli cytoplasmic membrane.     

Maternal Vitamin D Status and Offspring Bone Fractures: Prospective Study over Two Decades in Aarhus City,Denmark

Background

Studies investigating the association between maternal vitamin D status and offspring bone mass measured by dual-energy X-ray absorptiometry (DXA) during childhood have shown conflicting results.

Purpose

We used occurrence of bone fractures up to the age of 18 as a measure reflecting offspring bone mass and related that to maternal vitamin D status.

Methods

The Danish Fetal Origins 1988 Cohort recruited 965 pregnant women during 1988–89 at their 30^th gestation week antenatal midwife visit. A blood sample was drawn and serum was stored, which later was analyzed for the concentration of 25-hydroxyvitamin D (25(OH)D) by the liquid chromatography coupled with a tandem mass spectrometric method (LC-MS/MS). Outcome was diagnosis of first time bone fractures extracted from the Danish National Patient Register.

Results

Vitamin D status was available for 850 women. The median (5^th–95^th percentile) 25(OH)D was 76.2 (23.0–152.1) nmol/l. During follow up 294 children were registered with at least one bone fracture diagnosis. Multivariable Cox regression models using age as the underlying time scale indicated no overall association between maternal vitamin D status and first time bone fractures. However, there was a significantly increased hazard ratio (HR) during childhood for those who had maternal blood drawn in Dec/Jan/Feb compared with Jun/Jul/Aug (HR: 1.75, 95%CI: 1.11–2.74). Adjustment for vitamin D status strengthened this association (1.82, 1.12–2.97), which indicated a potential seasonal impact on offspring fractures independent of maternal vitamin D status. In a sensitivity analysis we found a borderline significant inverse association between continuous concentrations of 25(OH)D and offspring forearm fractures (P = 0.054).

Conclusion

Overall, our results did not substantiate an association between maternal vitamin D status and offspring bone fractures. Further studies on this subject are needed, but the study populations must be large enough to allow for subdivision of fractures.     

Seasonal sea ice cover as principal driver of spatial and temporal variation in depth extension and annual production of kelp in Greenland

We studied the depth distribution and production of kelp along the Greenland coast spanning Arctic to sub‐Arctic conditions from 78 ºN to 64 ºN. This covers a wide range of sea ice conditions and water temperatures, with those presently realized in the south likely to move northwards in a warmer future. Kelp forests occurred along the entire latitudinal range, and their depth extension and production increased southwards presumably in response to longer annual ice‐free periods and higher water temperature. The depth limit of 10% kelp cover was 9–14 m at the northernmost sites (77–78 ºN) with only 94–133 ice‐free days per year, but extended to depths of 21–33 m further south (73 ºN–64 ºN) where >160 days per year were ice‐free, and annual production of Saccharina longicruris and S. latissima, measured as the size of the annual blade, ranged up to sevenfold among sites. The duration of the open‐water period, which integrates light and temperature conditions on an annual basis, was the best predictor (relative to summer water temperature) of kelp production along the latitude gradient, explaining up to 92% of the variation in depth extension and 80% of the variation in kelp production. In a decadal time series from a high Arctic site (74 ºN), inter‐annual variation in sea ice cover also explained a major part (up to 47%) of the variation in kelp production. Both spatial and temporal data sets thereby support the prediction that northern kelps will play a larger role in the coastal marine ecosystem in a warmer future as the length of the open‐water period increases. As kelps increase carbon‐flow and habitat diversity, an expansion of kelp forests may exert cascading effects on the coastal Arctic ecosystem.     

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

Background

Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is generally referred to as Genotyping By Sequencing (GBS). To deal with GBS experimental design and initial processing specific bioinformatic tools are needed.

Results

GBSX is a package that assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, it performs optimized demultiplexing using these barcodes to create fastq files per barcode which can easily be plugged into existing variant analysis pipelines. Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.

Conclusions

GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.     

Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax

Background

In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stress, is less studied. In this study, we have estimated heritabilities of two growth traits (body weight and length) and of cortisol response to confinement stress in the European sea bass.

Findings

The F1 progeny analysed (n = 922) belonged to a small effective breeding population with contributions from an unbalanced family structure of just 10 males and 2 females. Heritability values ranged from 0.54 (±0.21) for body weight to 0.65 (±0.22) for standard body length and were low for cortisol response i.e. 0.08 (±0.06). Genetic correlations were positive (0.94) between standard body length and body weight and negative between cortisol and body weight and between cortisol and standard body length (−0.60 and −0.55, respectively).

Conclusion

This study confirms that in European sea bass, heritability of growth-related traits is high and that selection on such traits has potential. However, heritability of cortisol response to stress is low in European sea bass and since it is known to vary greatly among species, further studies are necessary to understand the reasons for these differences.     

Temporal Variation of Denitrification Activity in Plant-Covered, Littoral Sediment from Lake Hampen, Denmark

Diel and seasonal variations in denitrification were determined in a littoral lake sediment colonized by the perennial macrophyte Littorella uniflora (L.) Aschers. In the winter, the activity was low (5 μmol of N m⁻² h⁻¹) and was restricted to the uppermost debris layer at a depth of 0 to 1 cm. By midsummer, the activity increased to 50 μmol of N m⁻² h⁻¹ and was found throughout the root zone to a depth of 10 cm. The root zone accounted for as much as 50 to 70% of the annual denitrification. A significant release of organic substrates from the roots seemed to determine the high activities of root zone denitrification in the summer. The denitrification in the surface layer and in the root zone formed two distinct activity zones in the summer, when the root zone also contained nitrification activity, as indicated from the accumulations of NO₃⁻. Light conditions inhibited denitrification in both the surface layer and the upper part of the root zone, suggesting that a release of O₂ by benthic algae and from the roots of L. uniflora controlled a diel variation of denitrification. In midsummer, the rate of denitrification in both the surface layer and the upper part of the root zone was limited by NO₃⁻. In the growth season, there was evidence for a significant population of denitrifiers closely associated with the root surface.     

The movement protein of cucumber mosaic virus traffics into sieve elements in minor veins of nicotiana clevelandii

The location of the 3a movement protein (MP) of cucumber mosaic virus (CMV) was studied by quantitative immunogold labeling of the wild-type 3a MP in leaves of Nicotiana clevelandii infected by CMV as well as by using a 3a-green fluorescent protein (GFP) fusion expressed from a potato virus X (PVX) vector. Whether expressed from CMV or PVX, the 3a MP targeted plasmodesmata and accumulated in the central cavity of the pore. Within minor veins, the most extensively labeled plasmodesmata were those connecting sieve elements and companion cells. In addition to targeting plasmodesmata, the 3a MP accumulated in the parietal layer of mature sieve elements. Confocal imaging of cells expressing the 3a-GFP fusion protein showed that the 3a MP assembled into elaborate fibrillar formations in the sieve element parietal layer. The ability of 3a-GFP, expressed from PVX rather than CMV, to enter sieve elements demonstrates that neither the CMV RNA nor the CMV coat protein is required for trafficking of the 3a MP into sieve elements. CMV virions were not detected in plasmodesmata from CMV-infected tissue, although large CMV aggregates were often found in the parietal layer of sieve elements and were usually surrounded by 3a MP. These data suggest that CMV traffics into minor vein sieve elements as a ribonucleoprotein complex that contains the viral RNA, coat protein, and 3a MP, with subsequent viral assembly occurring in the sieve element parietal layer.     

Refinements of and commentary on the silver staining techniques of Fernández-Galiano

The original ammoniacal silver carbonate staining technique and subsequent modification developed by Fernández-Galiano are useful for investigating ciliate protozoan systematics and/or ciliate cortical structure and morphogenesis. The technique is complicated, however, by both uncertainties arising from the need to count drops of reagents and subjective control of the staining intensity. I have resolved these complications by defining volumes of reagents rather than using drops and by defining a range of staining times. I also comment on various steps of the techniques. My techniques are simplified and refined to produce consistent, high quality staining results.