Characterising the seasonal cycle of dissolved organic nitrogen using Cefas SmartBuoy high-resolution time-series samples from the southern North Sea

The Cefas SmartBuoy network provides a unique insight into the biogeochemical dynamics of the Northern European shelf seas, particularly the North Sea, through high-resolution automated offshore water sampling. We present total dissolved nitrogen and dissolved organic nitrogen (DON) from the Dowsing SmartBuoy site (53.531° N, 1.053° E) from January to October 2010, the first high resolution seasonal (winter-autumn) cycle of DON from the open North Sea. On top of a refractory background DON concentration of approximately 5 μM, a rapid increase in DON of a further ～5 μM is observed over the course of the spring bloom. This rapidly produced DON declines at an estimated net decay rate of between 0.6 and 1.8 μM month^?1. The slow decay suggests that the majority of the additional DON produced during the spring bloom is of semi-labile nature and has a lifetime of weeks to months. The dataset allows us to tightly constrain the budget for water column nitrogen over the winter, spring and summer of 2010 and clearly demonstrates the ‘sawtooth’ nature of the seasonal cycle of DON in the open North Sea, which has been impossible to resolve with a more traditional ship-based mode of operation. This work highlights the importance of autonomous sampling approaches in better understanding shelf sea biogeochemistry in the future.     

New insights into activation and substrate recognition of polyhydroxyalkanoate synthase from Ralstonia eutropha

The polyhydroxyalkanoate synthase of Ralstonia eutropha (PhaC_Re) shows a lag time for the start of its polymerization reaction, which complicates kinetic analysis of PhaC_Re. In this study, we found that the lag can be virtually eliminated by addition of 50 mg/L TritonX-100 detergent into the reaction mixture, as well as addition of 2.5 g/L Hecameg detergent as previously reported by Gerngross and Martin (Proc Natl Sci USA 92: 6279–6283, 1995). TritonX-100 is an effective lag eliminator working at much lower concentration than Hecameg. Kinetic analysis of PhaC_Re was conducted in the presence of TritonX-100, and PhaC_Re obeyed Michaelis–Menten kinetics for (R)-3-hydroxybutyryl-CoA substrate. In inhibitory assays using various compounds such as adenosine derivatives and CoA derivatives, CoA free acid showed competitive inhibition but other compounds including 3′-dephospho CoA had no inhibitory effect. Furthermore, PhaC_Re showed a considerably reduced reaction rate for 3′-dephospho (R)-3-hydroxybutyryl CoA substrate and did not follow typical Michaelis–Menten kinetics. These results suggest that the 3′-phosphate group of CoA plays a critical role in substrate recognition by PhaC_Re.     

High genetic diversity is not essential for successful introduction

Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.     

Evaluating Purifying Selection in the Mitochondrial DNA of Various Mammalian Species

Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.     

A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle

Analysis of data on 1000 Holstein-Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy-Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05-0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage disequilibrium. A total of 727 haplotype blocks consisting of > or =3 SNPs were identified. The average block length was 69.7 +/- 7.7 kb, which is approximately 5-10 times larger than in humans. These blocks comprised a total of 2964 SNPs and covered 50,638 kb of the sequence map, which constitutes 2.18% of the length of all autosomes. A set of tag SNPs, which will be useful for further fine-mapping studies, has been identified. Overall, the results suggest that as many as 75,000-100,000 tag SNPs would be needed to track all important haplotype blocks in the bovine genome. This would require approximately 250,000 SNPs in the discovery phase.     

Conserved regulation of MAP kinase expression by PUF RNA-binding proteins

Mitogen-activated protein kinase (MAPK) and PUF (for Pumilio and FBF [fem-3 binding factor]) RNA-binding proteins control many cellular processes critical for animal development and tissue homeostasis. In the present work, we report that PUF proteins act directly on MAPK/ERK-encoding mRNAs to downregulate their expression in both the Caenorhabditis elegans germline and human embryonic stem cells. In C. elegans, FBF/PUF binds regulatory elements in the mpk-1 3′ untranslated region (3′ UTR) and coprecipitates with mpk-1 mRNA; moreover, mpk-1 expression increases dramatically in FBF mutants. In human embryonic stem cells, PUM2/PUF binds 3′UTR elements in both Erk2 and p38α mRNAs, and PUM2 represses reporter constructs carrying either Erk2 or p38α 3′ UTRs. Therefore, the PUF control of MAPK expression is conserved. Its biological function was explored in nematodes, where FBF promotes the self-renewal of germline stem cells, and MPK-1 promotes oocyte maturation and germ cell apoptosis. We found that FBF acts redundantly with LIP-1, the C. elegans homolog of MAPK phosphatase (MKP), to restrict MAPK activity and prevent apoptosis. In mammals, activated MAPK can promote apoptosis of cancer cells and restrict stem cell self-renewal, and MKP is upregulated in cancer cells. We propose that the dual negative regulation of MAPK by both PUF repression and MKP inhibition may be a conserved mechanism that influences both stem cell maintenance and tumor progression.     

Analysis of control strategies for VIVA OpenHBM with active reflexive neck muscles

Modeling muscle activity in the neck muscles of a finite element (FE) human body model can be based on two biological reflex systems. One approach is to approximate the Vestibulocollic reflex (VCR) function, which maintains the head orientation relative to a fixed reference in space. The second system tries to maintain the head posture relative to the torso, similar to the Cervicocolic reflex (CCR). Strategies to combine these two neck muscle controller approaches in a single head-neck FE model were tested, optimized, and compared to rear-impact volunteer data. The first approach, Combined-Control, assumed that both controllers simultaneously controlled all neck muscle activations. In the second approach, Distributed-Control, one controller was used to regulate activation of the superficial muscles while a different controller acted on deep neck muscles. The results showed that any muscle controller that combined the two approaches was less effective than only using one of VCR- or CCR-based systems on its own. A passive model had the best objective rating for cervical spine kinematics, but the addition of a single active controller provided the best response for both head and cervical spine kinematics. The present study demonstrates the difficulty in completely capturing representative head and cervical spine responses to rear-impact loading and identified a controller capturing the VCR reflex as the best candidate to investigate whiplash injury mechanisms through FE modeling.

     

Dermatoglyphic variation in Europe

We describe the geographic variation patterns of 236 dermatoglyphic variables (118 for each sex) for 74 samples in Europe. Using principal components analysis and rotating to simple structure, we simplified these patterns to the first 20 axes, representing 74.2% of covariation. We then used heterogeneity tests, interpolated surfaces, one-dimensional and directional correlograms, and distances between correlograms to analyze the factor scores of these 20 axes. We also ordinated the 74 localities. The data are remarkable for showing little spatial autocorrelation, despite significant heterogeneity among localities. Only three factor axes exhibit consistently significant correlograms, indicating that there are few spatial patterns in the original variables in Europe. Almost all correlations between pairs of variables occur within serially homologous character sets and are thus developmentally determined. There is some support for demic diffusion from the southeast in finger patterns and ridge counts. We compare these results to those of previous studies and note that Lapps and Icelanders are outliers with respect to both genetics and finger tip variables, whereas Tatars are outliers with respect to craniometrics and dermatoglyphics. © 1996 Wiley-Liss, Inc.