Intra‐specific variability and plasticity influence potential tree species distributions under climate change

Aim To assess the effect of local adaptation and phenotypic plasticity on the potential distribution of species under future climate changes. Trees may be adapted to specific climatic conditions; however, species range predictions have classically been assessed by species distribution models (SDMs) that do not account for intra‐specific genetic variability and phenotypic plasticity, because SDMs rely on the assumption that species respond homogeneously to climate change across their range, i.e. a species is equally adapted throughout its range, and all species are equally plastic. These assumptions could cause SDMs to exaggerate or underestimate species at risk under future climate change. Location The Iberian Peninsula. Methods Species distributions are predicted by integrating experimental data and modelling techniques. We incorporate plasticity and local adaptation into a SDM by calibrating models of tree survivorship with adaptive traits in provenance trials. Phenotypic plasticity was incorporated by calibrating our model with a climatic index that provides a measure of the differences between sites and provenances. Results We present a new modelling approach that is easy to implement and makes use of existing tree provenance trials to predict species distribution models under global warming. Our results indicate that the incorporation of intra‐population genetic diversity and phenotypic plasticity in SDMs significantly altered their outcome. In comparing species range predictions, the decrease in area occupancy under global warming conditions is smaller when considering our survival–adaptation model than that predicted by a ‘classical SDM’ calibrated with presence–absence data. These differences in survivorship are due to both local adaptation and plasticity. Differences due to the use of experimental data in the model calibration are also expressed in our results: we incorporate a null model that uses survival data from all provenances together. This model always predicts less reduction in area occupancy for both species than the SDM calibrated with presence–absence. Main conclusions We reaffirm the importance of considering adaptive traits when predicting species distributions and avoiding the use of occurrence data as a predictive variable. In light of these recommendations, we advise that existing predictions of future species distributions and their component populations must be reconsidered.     

Evaluating the influence of off-shore cage aquaculture on the benthic ecosystem in Alghero Bay (Sardinia,Italy) using AMBI and M-AMBI

The impact of an off-shore fish farm in Alghero Bay (northwest Sardinia, Italy) on the benthic ecosystem was investigated in 2007 and 2008. In addition to studying the chemical and physical characteristics of the area (i.e., currents and sediment analyses), some biological analyses were also performed. The AZTI's Marine Biotic Index (AMBI) and the multivariate AMBI (M-AMBI) were calculated, which are being used in assessing the ecological status of benthic communities within the European Water Framework Directive (WFD). Clear impact gradients were detected according to both methods; they are related to farm production, prevailing currents, and characteristics of the area (i.e., water depth and distance to the cages). The site affected most was detected within 84 m from the cages; the area that no longer showed effects was over 907 m from the cages. The gradient is shown by decreasing AMBI values and percentage of opportunistic species and increasing richness, diversity, and the presence of sensitive species. This study highlights the importance of setting reference conditions for different areas when calculating M-AMBI. These reference conditions correspond to those in undisturbed sites in the opposite direction of the prevailing currents within the area.     

Remote sensing data predict indicators of soil functioning in semi-arid steppes,central Spain

A substantial part of current research efforts on desertification are devoted to establish monitoring systems to evaluate the status of natural resources and the onset of desertification processes. Methodologies based on ground-collected soil and plant indicators are being increasingly used for this aim because they are affordable yet do not compromise accuracy. Despite their inherent value, these methods have limitations regarding the extent of the area that can be monitored using them. Such limitations can be overcome combining field-based approaches with remote sensing data, which allow the establishment of monitoring programs over large areas. In this article we tested the relationship between a field methodology based on indicators of ecosystem functioning, the landscape function analysis (LFA), and a vegetation index (NDVI) obtained from satellite images of the ASTER sensor using data gathered in Stipa tenacissima steppes from central Spain. LFA uses soil surface indicators to assess the condition of a given ecosystem by producing three numerical indices (stability, infiltration and nutrient cycling) reflecting the status of basic soil functions. We found a significant positive linear relationship between the NDVI, the three LFA indices and some key structural attributes of vegetation related to the cover of perennial plants. Our results indicate that NDVI can be used as a surrogate of ecosystem functioning in semi-arid Mediterranean steppes, and thus can be a helpful index to monitor the functional status of large areas in these ecosystems, and the possible onset of desertification processes.     

Academic and molecular matrices: a study of the transformations of connective tissue research at the University of Manchester (1947-1996)

This paper explores the different identities adopted by connective tissue research at the University of Manchester during the second half of the 20th century. By looking at the long-term redefinition of a research programme, it sheds new light on the interactions between different and conflicting levels in the study of biomedicine, such as the local and the global, or the medical and the biological. It also addresses the gap in the literature between the first biomedical complexes after World War II and the emergence of biotechnology. Connective tissue research in Manchester emerged as a field focused on new treatments for rheumatic diseases. During the 1950s and 60s, it absorbed a number of laboratory techniques from biology, namely cell culture and electron microscopy. The transformations in scientific policy during the late 70s and the migration of Manchester researchers to the US led them to adopt recombinant DNA methods, which were borrowed from human genetics. This resulted in the emergence of cell matrix biology, a new field which had one of its reference centres in Manchester. The Manchester story shows the potential of detailed and chronologically wide local studies of patterns of work to understand the mechanisms by which new biomedical tools and institutions interact with long-standing problems and existing affiliations.     

An assessment of the ultrasonic probe-based enhancement of protein cleavage with immobilized trypsin

The use of ultrasonic probe, in conjunction with immobilized trypsin, has been explored in this work for potential enhancement of protein digestion. Several solid supports commonly used to immobilize trypsin were subjected to different ultrasonication amplitudes and time in order to investigate their mechanical resistance to ultrasonic energy when provided by the ultrasonic probe. Glass beads and magnetic particles were found to remain intact in most conditions studied. It was found that immobilized trypsin cannot be reused after ultrasonication since the enzymatic activity was greatly diminished. For comparative purposes, vortex shaking was also explored for protein cleavage. Four standard proteins--bovine serum albumin, α-lactalbumin, carbonic anhydrase and ovalbumin--were successfully identified using peptide mass fingerprint, or peptide fragment fingerprint. In addition, the performance of the classical protein cleavage (overnight, 12 h) and the ultrasonic methods was found to be similar when the digestion of a complex proteome, human plasma, was assessed through 18-O quantification. The digestion yields found were 90-117% for the ultrasonic and 5-21% for the vortex when those methods were compared with the classical overnight digestion.     

Membrane proteomic signatures of karyotypically normal and abnormal human embryonic stem cell lines and derivatives

Cultured human embryonic stem cells (hESCs) and derived derivatives contain heterogeneous cell populations with varying degrees of differentiation and karyotypic stability. The inability to isolate homogenous population presents a challenge toward cell-based applications and therapies. A proteomics approach was utilized to discover novel membrane proteins able to distinguish between the hESC lines BG01, WA09, and abBG02 (trisomy 12, 14, 17 and an extra copy of the X chromosome), along with WA09-derived human neural progenitor (hNP) cells. Membrane protein signatures were developed using sucrose-gradient isolation, 1-D gel electrophoresis followed by in-gel digestion and analysis by reverse phase chromatography coupled to ion trap-FT-ICR. At a ≤1.0% false discovery rate, 1918 proteins were identified; 775 were annotated as membrane proteins and 720 predicted to contain transmembrane spanning regions. Flow cytometry was used to validate cell surface expression of selected proteins. Junctional adhesion molecule 1 expression was shared by BG01, BG02 and abBG02 hESC lines. Dysferlin expression was specific to the WA09 hESC line and not the derived neural or mesenchymal progenitors. Ciliary neurotrophic factor receptor distinguished WA09-derived human neural progenitor cells from the parent hESC population, and WA09-derived mesenchymal progenitor cells. This study expands the current membrane protein data set for hESCs.     

Long-term betacarotene-supplementation enhances serum insulin concentrations without effect on the onset of puberty in the female goat

The effect of betacarotene (BC) supplementation on the onset of puberty and serum insulin levels in goats was evaluated in the study. In June, prepuberal goats (n=17; 3 months old; 7/8 Saanen-Alpine; 26° NL) were randomly assigned to one of two groups: 1/ betacarotene group supplemented daily with 50 mg of BC (n=9; live weight [LW]: 17.3±1.0 kg; body condition score [BCS]: 3.34±0.12) or 2/ control group (CONT; n=8; LW:16.1±1.0 kg; BCS=3.17±0.12). From June to November, an intermittent blood sampling was performed twice per week in both groups to evaluate serum progesterone (P(4)), while monthly samples were intended for insulin (INS) determination. Initial mean LW (16.7±1.0 kg) and BCS (3.31±0.12) were similar (p>0.05) in both groups. Mean serum insulin (1.37 vs. 1.18±0.09 ng/ml), age of puberty (215.7 vs. 226.5±6.6 days) and the percentage of goats reaching puberty (44.4 vs. 25.0±17.0%) did not differ (p>0.05) between BC and CONT group, respectively. However, increase in serum insulin during the second half of the experiment was observed in BC group (p<0.05) which was positively correlated with LW (r=0.95; p<0.05). In addition, as LW (r=-0.89) and serum insulin (r=-0.76) levels increased, the natural photoperiod decreased, revealing negative correlations (p<0.05) between the respective variables. In this study, BC supplementation did not promote precocious puberty and did not affect the percentage of goats reaching activation of the hypothalamic-hypophyseal-gonadal axis during the establishment of puberty. Nonetheless, BC supplementation positively affected the release pattern of insulin suggesting a potential role of BC as pancreas-activating molecule.     

Complete genome sequence of Hirschia baltica type strain (IFAM 1418(T))

The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. baltica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacterium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 protein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.     

A genome-wide association study of the Protein C anticoagulant pathway

The Protein C anticoagulant pathway regulates blood coagulation by preventing the inadequate formation of thrombi. It has two main plasma components: protein C and protein S. Individuals with protein C or protein S deficiency present a dramatically increased incidence of thromboembolic disorders. Here, we present the results of a genome-wide association study (GWAS) for protein C and protein S plasma levels in a set of extended pedigrees from the Genetic Analysis of Idiopathic Thrombophilia (GAIT) Project. A total number of 397 individuals from 21 families were typed for 307,984 SNPs using the Infinium® 317 k Beadchip (Illumina). Protein C and protein S (free, functional and total) plasma levels were determined with biochemical assays for all participants. Association with phenotypes was investigated through variance component analysis. After correcting for multiple testing, two SNPs for protein C plasma levels (rs867186 and rs8119351) and another two for free protein S plasma levels (rs1413885 and rs1570868) remained significant on a genome-wide level, located in and around the PROCR and the DNAJC6 genomic regions respectively. No SNPs were significantly associated with functional or total protein S plasma levels, although rs1413885 from DNAJC6 showed suggestive association with the functional protein S phenotype, possibly indicating that this locus plays an important role in protein S metabolism. Our results provide evidence that PROCR and DNAJC6 might play a role in protein C and free protein S plasma levels in the population studied, warranting further investigation on the role of these loci in the etiology of venous thromboembolism and other thrombotic diseases.     

The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation

Background

The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B.

Methodology/Principal Findings

As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212–216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers.

Conclusions/Significance

Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B'' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation.