Future land use effects on the connectivity of protected area networks in southeastern Spain

Land-use change is a major driver of the global biodiversity crisis, mainly via the fragmentation and loss of natural habitat. Although land-use changes will accelerate to meet humankind's growing demand for agricultural products, conservation planning rarely considers future land uses and how they may affect the connectivity of ecological networks. Here, we integrate land-use models with landscape fragmentation and connectivity analyses, to assess the effects of past and future land-use changes on the connectivity of protected area networks for a highly dynamic region in southeast Spain. Our results show a continued geographical polarisation of land use, with agricultural intensification and urban development in the coastal areas, and the abandonment of traditional land use in the mountains (e.g., 1100 km² of natural vegetation are projected to be lost in coastal areas whereas 32 km² of natural vegetation would recover in interior areas from 1991 to 2015). As a result, coastal protected areas will experience increasing isolation. The connectivity analyses reveal that the two protected area networks in place in the study area, the European “Natura 2000” and the Andalusian “RENPA” networks, include many landscape connectors. However, we identify two areas that currently lack protection but contain several important patches for maintaining the region's habitat connectivity: the northwestern and the southwestern slopes of the Sierra Cabrera and Bédar protected area. Our results highlight the importance of considering future land-use trajectories in conservation planning to maintain connectivity at the regional scale, and to improve the resilience of conservation networks.     

Viremia and antibody response in green monkeys (Chlorocebus aethiops sabaeus) infected with dengue virus type 2: A potential model for vaccine testing

The increasingly limited availability and high cost of the hitherto most commonly used monkey species in dengue vaccine research has augmented the importance of identifying alternative suitable models for these studies. In this study we examined the capacity of green monkeys ( Chlorocebus aethiops sabaeus ) to develop dengue viremia, and thus provide a potential model for dengue vaccine testing. Monkeys were inoculated with two different doses of dengue virus type 2. All animals in both groups became viremic after inoculation of the virus. In the lower dose group, mean viremia duration of 5.66 days was detected, whereas in the group that received the 10⁶ PFU dose, viremia had a mean duration of only 1.66 days. Antibody titers were similar to those obtained in previous experiments with rhesus and cynomolgus macaques. We conclude that green monkeys develop viremia and antibody responses and therefore provide a potential model for the preclinical evaluation of novel candidates for dengue vaccines.     

Central B-cell tolerance: where selection begins

The development of an adaptive immune system based on the random generation of antigen receptors requires a stringent selection process that sifts through receptor specificities to remove those reacting with self-antigens. In the B-cell lineage, this selection process is first applied to IgM⁺ immature B cells. By using increasingly sophisticated mouse models, investigators have identified the central tolerance mechanisms that negatively select autoreactive immature B cells and prevent inclusion of their antigen receptors into the peripheral B-cell pool. Additional studies have uncovered mechanisms that promote the differentiation of nonautoreactive immature B cells and their positive selection into the peripheral B-cell population. These mechanisms of central selection are fundamental to the generation of a naïve B-cell repertoire that is largely devoid of self-reactivity while capable of reacting with any foreign insult.B-cell generation in the bone marrow of adult mammals occurs through a tightly controlled developmental process (Fig. 1). Productive rearrangement of immunoglobulin heavy (IgH) and light (IgL) chain gene segments in B lymphocyte precursor cells, in addition to the expression of Ig-α (CD79a) and Ig-β (CD79b), result in the generation and expression on the cell surface of a mature B-cell antigen receptor (BCR). Whereas the combination of Ig H and L chains determines the antigenic specificity of the newly formed BCR, their association with Ig-α and Ig-β allows transduction of a signal inside the cell that directs cell fate. Developing B cells first express a mature BCR on the cell surface in the form of IgM and as such are classified as immature B cells (Fig. 1) (Hardy et al. 1991; Pelanda et al. 1996). It is at the immature B-cell stage that the BCR is tested for the first time for reactivity against autoantigens. This test determines whether the immature B cell and the antibody it expresses on the surface will be selected into the peripheral B-cell repertoire. Central B-cell tolerance, in fact, refers to the process that negatively selects newly generated immature B cells that react with a self-antigen in the bone marrow environment. This is considered the first checkpoint of B-cell tolerance, and the results of this checkpoint are fundamental to the generation of a naïve repertoire that contains foreign reactive antibodies and is largely devoid of self-reactive specificities.Open in a separate windowFigure 1.Schematic representation of B-cell development and Ig loci in mice. Large pro-B cells initiate Ig gene rearrangement at the IgH locus. Expression of a H chain following a productive V_HD_HJ_H recombination event promotes the differentiation of large pre-B cells in which the expression of pre-BCR (H chain pairing with surrogate light chains) results in the clonal expansion of H chain-positive pre-B cells and the development of small pre-B cells. Expression of conventional L chains following productive rearrangements at the IgL chain loci in small pre-B cells promotes the development of a diverse population of IgM⁺ immature B cells, which then differentiate into IgM⁺IgD⁺ transitional B cells. The scheme of mouse Ig H, κ, and λ loci (not to scale) indicate the presence of V (white rectangles), D (black vertical lines), J (brown vertical lines; a dashed line indicates a nonfunctional element), and C (black rectangles; a gray rectangle indicates a nonfunctional element) gene segments. The scheme does not represent the number of V_H, D_H, and Vκ gene segments in the actual Ig loci.On passing this central checkpoint, immature B cells continue to differentiate into transitional and mature B cells before and after they travel to the spleen (Loder et al. 1999; Allman et al. 2001; Su and Rawlings 2002; Tarlinton et al. 2003). Analysis of the bone marrow early immature B-cell repertoire indicates that a staggering 50%–75% of these cells express BCRs that are specific for self-antigens, both in mice and humans (Grandien et al. 1994; Wardemann et al. 2003). Similar studies performed on cell populations at the other end of this central checkpoint, namely, transitional and naïve mature B cells in spleen and blood, show a much lower frequency (20%–40%) of cells expressing autoreactive antibodies (Grandien et al. 1994; Wardemann et al. 2003), demonstrating the stringency and limitation of this initial selection step. Moreover, individuals affected by autoimmune disease such as lupus erythematosus or rheumatoid arthritis bear many more autoreactive cells in their new emigrant and naïve B-cell populations (Samuels et al. 2005; Yurasov et al. 2005), indicating a defect in central (and/or peripheral) B-cell selection. Thus, it seems important that the development of autoreactive immature B cells be constrained to prevent the potential occurrence of autoimmunity. However, there are also reasons to believe that the high frequency of autoreactive specificities generated during primary Ig gene rearrangements may be necessary for the generation of the peripheral B-cell repertoire (Pelanda et al. 1997; Kohler et al. 2008). Indeed, a fraction of autoreactive immature B cells, those manifesting a low level of self-reactivity, do bypass the central checkpoint of tolerance and differentiate into mature B cells (Hayakawa et al. 2003; Wardemann et al. 2003; Wen et al. 2005). The inclusion of these weakly self-reactive B cells in the peripheral B-cell repertoire may allow recognition of a broader spectrum of foreign molecules, potentially decreasing the negative impact of infections, especially at early stages (Mouquet et al. 2010).What are the rules that govern the selection of immature B cells? Most studies of central tolerance have been conducted by following the selection of B cells expressing BCRs displaying well-defined reactivity for natural or synthetic self-antigens. This has been accomplished through the use of Ig transgenic mice in which developing B cells have been altered to carry prerearranged Ig H and L chain genes encoding antibodies of defined antigen specificity and reactivity. Here we review some of these studies, what we have learned from them, and open questions that still await answers.     

Increasing calling accuracy,coverage, and read-depth in sequence data by the use of haplotype blocks

High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing genotyping technologies when resources are limited. In this work, we are proposing a new imputation pipeline (“HBimpute”) that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data. The key idea of the pipeline is the use of haplotype blocks from the software HaploBlocker to identify locally similar lines and subsequently use the reads of all locally similar lines in the variant calling for a specific line. The effectiveness of the pipeline is showcased on a dataset of 321 doubled haploid lines of a European maize landrace, which were sequenced at 0.5X read-depth. The overall imputing error rates are cut in half compared to state-of-the-art software like BEAGLE and STITCH, while the average read-depth is increased to 83X, thus enabling the calling of copy number variation. The usefulness of the obtained imputed data panel is further evaluated by comparing the performance of sequence data in common breeding applications to that of genomic data generated with a genotyping array. For both genome-wide association studies and genomic prediction, results are on par or even slightly better than results obtained with high-density array data (600k). In particular for genomic prediction, we observe slightly higher data quality for the sequence data compared to the 600k array in the form of higher prediction accuracies. This occurred specifically when reducing the data panel to the set of overlapping markers between sequence and array, indicating that sequencing data can benefit from the same marker ascertainment as used in the array process to increase the quality and usability of genomic data.     

Translating niche features: Modelling differential exposure of Argentine reptiles to global climate change

Global climate change affects the distributions of ectotherms and may be the cause of several conservation problems, such as great displacement of climatic suitable spaces for species and, consequently, important reductions of the extent of liveable places, threatening the existence of many of them. Species exposure (and hence vulnerability) to global climate change is linked to features of their climatic niches (such as the relative position of the inhabited localities of each species in the climatic space), and therefore to characteristics of their geographic ranges (such as the extent of the distributions or altitudinal range inhabited by the species). In order to analyze the pattern of response of Argentine reptiles to global climate change, we ran phylogenetic generalized least squares models using species exposure to global climate change as a response variable, and (i) niche properties (breadth and position of the species in the climate space) and (ii) general features of the distribution of species (maximum latitude, altitudinal range, maximum elevation, distributional range and proximity to the most important dispersal barrier) as predictors. Our results suggest that the best way to explain climate change exposure is by combining breadth and position of climatic niche of the species or combining geographic features that are indicators of both niche characteristics. Our best model shows that in our study area, species with the narrowest distributional ranges that also inhabit the highest elevations are the most exposed to the effects of global climate change. In this sense, reptile species from Yungas, Puna and Andes ecoregions could be especially vulnerable to the effects of climate change. We believe that these types of models may represent an interesting tool for determining species and places particularly threatened by the effects of global climate change, which should be strongly considered in conservation planning.     

Tracking Nutrient Routing in Avian Consumers in a Subtropical Desert

The nutrients animals ingest are allocated to serve different functions. We used contrasting C stable isotope signatures of dominant vegetation types in a North American subtropical desert to decipher how avian consumers allocate nutrients to fuel oxidative metabolism and to construct tissues. We conducted C stable isotope analysis of breath and feathers collected from nectarivores (hummingbirds) and of breath, plasma, and red blood cell samples collected from frugivores, granivores, and insectivores. Based on varying nutrient characteristics of food sources, we expected that for frugivores and granivores, CAM‐derived food (RC_CAM) would have similar importance for oxidative metabolism and for tissue building, that RC_CAM in nectarivores and insectivores would be more important for fueling metabolism than for generating tissues, and that (although low) RC_CAM in insectivores would be higher for sustaining metabolism than for building tissues. Our predictions held true for nectarivores and granivores, but RC_CAM use in tissue building was lower than expected in frugivores and higher than expected in insectivores. Our examination at the trophic guild, population, and individual levels showed that in general, nutrients used to sustain oxidative metabolism and tissue construction had a uniform isotopic origin. This finding suggests that the avian community under investigation does not route different food groups to fulfill different needs. However, we found some exceptions, indicating that birds can use different food sources for different functions, irrespective of trophic guild.     

Development and preliminary evaluation of a 90?K Axiom? SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

Background

A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.

Results

About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.

Conclusions

The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1310-1) contains supplementary material, which is available to authorized users.     

Characterization of the rRNA locus of Pfiesteria piscicida and development of standard and quantitative PCR-based detection assays targeted to the nontranscribed spacer

Pfiesteria piscicida is a heterotrophic dinoflagellate widely distributed along the middle Atlantic shore of the United States and associated with fish kills in the Neuse River (North Carolina) and the Chesapeake Bay (Maryland and Virginia). We constructed a genomic DNA library from clonally cultured P. piscicida and characterized the nontranscribed spacer (NTS), small subunit, internal transcribed spacer 1 (ITS1), 5.8S region, ITS2, and large subunit of the rRNA gene cluster. Based on the P. piscicida ribosomal DNA sequence, we developed a PCR-based detection assay that targets the NTS. The assay specificity was assessed by testing clonal P. piscicida and Pfiesteria shumwayae, 35 additional dinoflagellate species, and algal prey (Rhodomonas sp.). Only P. piscicida and nine presumptive P. piscicida isolates tested positive. All PCR-positive products yielded identical sequences for P. piscicida, suggesting that the PCR-based assay is species specific. The assay can detect a single P. piscicida zoospore in 1 ml of water, 10 resting cysts in 1 g of sediment, or 10 fg of P. piscicida DNA in 1 micro g of heterologous DNA. An internal standard for the PCR assay was constructed to identify potential false-negative results in testing of environmental sediment and water samples and as a competitor for the development of a quantitative competitive PCR assay format. The specificities of both qualitative and quantitative PCR assay formats were validated with >200 environmental samples, and the assays provide simple, rapid, and accurate methods for the assessment of P. piscicida in water and sediments.     

Hydralazine and Organic Nitrates Restore Impaired Excitation-Contraction Coupling by Reducing Calcium Leak Associated with Nitroso-Redox Imbalance

Although the combined use of hydralazine and isosorbide dinitrate confers important clinical benefits in patients with heart failure, the underlying mechanism of action is still controversial. We used two models of nitroso-redox imbalance, neuronal NO synthase-deficient (NOS1^−/−) mice and spontaneously hypertensive heart failure rats, to test the hypothesis that hydralazine (HYD) alone or in combination with nitroglycerin (NTG) or isosorbide dinitrate restores Ca²⁺ cycling and contractile performance and controls superoxide production in isolated cardiomyocytes. The response to increased pacing frequency was depressed in NOS1^−/− compared with wild type myocytes. Both sarcomere length shortening and intracellular Ca²⁺ transient (Δ[Ca²⁺]_i) responses in NOS1^−/− cardiomyocytes were augmented by HYD in a dose-dependent manner. NTG alone did not affect myocyte shortening but reduced Δ[Ca²⁺]_i across the range of pacing frequencies and increased myofilament Ca²⁺ sensitivity thereby enhancing contractile efficiency. Similar results were seen in failing myocytes from the heart failure rat model. HYD alone or in combination with NTG reduced sarcoplasmic reticulum (SR) leak, improved SR Ca²⁺ reuptake, and restored SR Ca²⁺ content. HYD and NTG at low concentrations (1 μm), scavenged superoxide in isolated cardiomyocytes, whereas in cardiac homogenates, NTG inhibited xanthine oxidoreductase activity and scavenged NADPH oxidase-dependent superoxide more efficiently than HYD. Together, these results revealed that by reducing SR Ca²⁺ leak, HYD improves Ca²⁺ cycling and contractility impaired by nitroso-redox imbalance, and NTG enhanced contractile efficiency, restoring cardiac excitation-contraction coupling.     

The effect of binding of spider-derived antimicrobial peptides, oxyopinins, on lipid membranes

Oxyopinins (Oxki1 and Oxki2) are antimicrobial peptides isolated from the crude venom of the wolf spider Oxyopes kitabensis. The effect of oxyopinins on lipid bilayers was investigated using high-sensitivity titration calorimetry and ³¹P solid-state NMR spectroscopy. High-sensitivity titration calorimetry experiments showed that the binding of oxyopinins was exothermic, and the binding enthalpies (ΔH) to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) small unilamellar vesicles (SUVs) were − 18.1 kcal/mol and − 15.0 kcal/mol for Oxki1 and Oxki2, respectively, and peptide partition coefficient (K_p) was found to be 3.9 × 10³ M^− 1. ³¹P NMR spectra of 1,2-dielaidoyl-sn-glycero-3-phosphoethanolamine (DEPE) membranes in the presence of oxyopinins indicated that they induced a positive curvature in lipid bilayers. The induced positive curvature was stronger in the presence of Oxki2 than in the presence of Oxki1. ³¹P NMR spectra of phosphaditylcholine (PC) membranes in the presence of Oxki2 showed that Oxki2 produced micellization of membranes at low peptide concentrations, but unsaturated PC membranes or acidic phospholipids prevented micellization from occurring. Furthermore, ³¹P NMR spectra using membrane lipids from E. coli suggested that Oxki1 was more disruptive to bacterial membranes than Oxki2. These results strongly correlate to the known biological activity of the oxyopinins.