Improving the quality of protein structure models by selecting from alignment alternatives

Background  

In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from inferior models. Here, we propose a new method to use an MQAP to improve the quality of models. With a given target sequence and template structure, we construct a number of different alignments and corresponding models for the sequence. The quality of these models is scored with an MQAP and used to choose the most promising model. An SVM-based selection scheme is suggested for combining MQAP partial potentials, in order to optimize for improved model selection.     

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2‐acidified sea water

Ocean acidification is the increase in seawater pCO₂ due to the uptake of atmospheric anthropogenic CO₂, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO₂, and associated decrease in pH, represents a climate change‐related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal‐level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular‐level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild‐caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA‐seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms.     

Spring bloom dynamics in Kongsfjorden,Svalbard: nutrients,phytoplankton, protozoans and primary production

The marine ecosystem in Kongsfjorden (79°N), a glacial fjord in Svalbard, is to a large extent well known with regard to hydrography, mesozooplankton and higher trophic levels. Research on primary production and lower trophic levels is still scare and especially investigations from winter and spring periods. The spring bloom dynamics in Kongsfjorden were investigated in 2002. The development in nutrient conditions, phytoplankton, protozoans and primary production were followed from 15 April until 22 May. The winter/spring in 2002 was categorized as a cold year with sea ice cover and water masses dominated by local winter-cooled water. The spring bloom started around 18 April and lasted until the middle of May. The bloom probably peaked in late April, but break-up of sea ice made it impossible to sample frequently in this period. Diatoms dominated the phytoplankton assemblage. We estimated the total primary production during the spring bloom in 2002 to range 27–35 g C m⁻². There was a mismatch situation between the mesozooplankton and the phytoplankton spring bloom in 2002.     

DNA barcoding of the northern Northeast Atlantic skates (Chondrichthyes,Rajiformes), with remarks on the widely distributed starry ray

The skate fauna in the northern Northeast (NE) Atlantic is poorly investigated, and misidentifications are common. Here, ‘DNA barcoding’ was used to analyse 105 specimens of 15 species previously reported from the area to investigate the occurrence of species. Of these 15 species, three were new to the region and confirmed with voucher specimens. Three previously reported taxa were not obtained from the study area, providing a total number of 12 skate species for the northern NE Atlantic. Only one specimen of the critically endangered Dipturus batis complex was found. It occurs frequently in the literature and commercial fisheries catch records, and we argue that the vast majority of these are misidentifications. Due to striking differences in Amblyraja radiata life history parameters across the North Atlantic, cryptic species diversity has previously been suspected. A total of 80 A. radiata cytochrome c oxidase subunit I sequences from across the North Atlantic were sampled, and the highest fixation index (F_ST) was found when maximising geographical distance (F_ST = 0.133). A lower index was found when grouped according to life history (F_ST = 0.067). These results are not strongly supportive for the occurrence of cryptic species.     

Lipids and fatty acids in ice algae and phytoplankton from the Marginal Ice Zone in the Barents Sea

Samples of ice algae from the Marginal Ice Zone in the Barents Sea could be divided into two categories: one dominated by assemblages of Melosira arctica, and the other dominated by Nitzschia frigida and associated diatoms. Total lipid from the Melosira assemblages consisted of approximately equal amounts of polar lipids and triacylglycerols. Total lipid from the Nitzschia assemblages contained more triacylglycerols than polar lipids. Total lipid from the Melosira assemblages had higher percentages of C16 PUFA, especially 16:4(n-1) and 20:5(n-3), than that from the Nitzschia assemblages, this reflecting the higher percentages of both C16 PUFA and 20:5(n-3) in polar lipids than in triacylglycerols. Phytoplankton from the pelagic zone were␣richer in flagellates and contained less C16 PUFA and 20:5(n-3) but more C18 PUFA and 22:6(n-3). The dominance of diatoms in the ice-algae assemblages in the Marginal Ice Zone and their high nutritional value as a source of 20:5(n-3) for higher trophic levels are emphasised. Received: 24 November 1997 / Accepted: 8 February 1998