Projecting terrestrial biodiversity intactness with GLOBIO 4

Scenario-based biodiversity modelling is a powerful approach to evaluate how possible future socio-economic developments may affect biodiversity. Here, we evaluated the changes in terrestrial biodiversity intactness, expressed by the mean species abundance (MSA) metric, resulting from three of the shared socio-economic pathways (SSPs) combined with different levels of climate change (according to representative concentration pathways [RCPs]): a future oriented towards sustainability (SSP1xRCP2.6), a future determined by a politically divided world (SSP3xRCP6.0) and a future with continued global dependency on fossil fuels (SSP5xRCP8.5). To this end, we first updated the GLOBIO model, which now runs at a spatial resolution of 10 arc-seconds (~300 m), contains new modules for downscaling land use and for quantifying impacts of hunting in the tropics, and updated modules to quantify impacts of climate change, land use, habitat fragmentation and nitrogen pollution. We then used the updated model to project terrestrial biodiversity intactness from 2015 to 2050 as a function of land use and climate changes corresponding with the selected scenarios. We estimated a global area-weighted mean MSA of 0.56 for 2015. Biodiversity intactness declined in all three scenarios, yet the decline was smaller in the sustainability scenario (-0.02) than the regional rivalry and fossil-fuelled development scenarios (-0.06 and -0.05 respectively). We further found considerable variation in projected biodiversity change among different world regions, with large future losses particularly for sub-Saharan Africa. In some scenario-region combinations, we projected future biodiversity recovery due to reduced demands for agricultural land, yet this recovery was counteracted by increased impacts of other pressures (notably climate change and road disturbance). Effective measures to halt or reverse the decline of terrestrial biodiversity should not only reduce land demand (e.g. by increasing agricultural productivity and dietary changes) but also focus on reducing or mitigating the impacts of other pressures.Peer reviewe

Toll-Like Receptor Family Polymorphisms Are Associated with Primary Renal Diseases but Not with Renal Outcomes Following Kidney Transplantation

Toll-like receptors (TLRs) play a crucial role in innate- and adaptive immunity. The TLR pathways were shown to play key functional roles in experimental acute and chronic kidney injury, including the allo-immune response after experimental renal transplantation. Data about the precise impact of TLRs and their negative regulators on human renal transplant outcomes however are limited and contradictory. We studied twelve non-synonymous single nucleotide polymorphisms (SNPs) of which eleven in TLR1-8 and one in SIGIRR in a final cohort comprising 1116 matching donors and recipients. TLR3 p.Leu412Phe and SIGIRR p.Gln312Arg significantly deviated from Hardy-Weinberg equilibrium and were excluded. The frequency distribution of the minor alleles of the remaining 10 TLR variants were compared between patients with end-stage renal disease (recipients) and controls (kidney donors) in a case-control study. Secondly, the associations between the minor allele frequency of the TLR variants and delayed graft function, biopsy-proven acute rejection and death-censored graft failure after transplantation were investigated with Cox regression. Carrier frequencies of the minor alleles of TLR1 p.His305Leu (OR = 4.79, 95% CI = 2.35-9.75, P = 0.0002), TLR1 p.Asn248Ser (OR = 1.26, 95% CI = 1.07-1.47, P = 0.04) and TLR8 p.Met1Val (OR = 1.37, 95% CI = 1.14-1.64, P = 0.008) were significantly higher in patients with ESRD, with little specificity for the underlying renal disease entity (adjusted for age, gender and donor-recipient relatedness). The minor allele frequency of none of the TLR variants significantly associated with the surrogate and definite outcomes, even when multivariable models were created that could account for TLR gene redundancy. In conclusion, genetic variants in TLR genes were associated with the prevalence of ESRD but not renal transplant outcomes. Therefore, our data suggests that specific TLR signaling routes might play a role in the final common pathway of primary renal injury. A role for TLR signaling in the context of renal transplantation is probably limited

Projecting terrestrial biodiversity intactness with GLOBIO 4

Scenario-based biodiversity modelling is a powerful approach to evaluate how possible future socio-economic developments may affect biodiversity. Here, we evaluated the changes in terrestrial biodiversity intactness, expressed by the mean species abundance (MSA) metric, resulting from three of the shared socio-economic pathways (SSPs) combined with different levels of climate change (according to representative concentration pathways [RCPs]): a future oriented towards sustainability (SSP1xRCP2.6), a future determined by a politically divided world (SSP3xRCP6.0) and a future with continued global dependency on fossil fuels (SSP5xRCP8.5). To this end, we first updated the GLOBIO model, which now runs at a spatial resolution of 10 arc-seconds (~300 m), contains new modules for downscaling land use and for quantifying impacts of hunting in the tropics, and updated modules to quantify impacts of climate change, land use, habitat fragmentation and nitrogen pollution. We then used the updated model to project terrestrial biodiversity intactness from 2015 to 2050 as a function of land use and climate changes corresponding with the selected scenarios. We estimated a global area-weighted mean MSA of 0.56 for 2015. Biodiversity intactness declined in all three scenarios, yet the decline was smaller in the sustainability scenario (-0.02) than the regional rivalry and fossil-fuelled development scenarios (-0.06 and -0.05 respectively). We further found considerable variation in projected biodiversity change among different world regions, with large future losses particularly for sub-Saharan Africa. In some scenario-region combinations, we projected future biodiversity recovery due to reduced demands for agricultural land, yet this recovery was counteracted by increased impacts of other pressures (notably climate change and road disturbance). Effective measures to halt or reverse the decline of terrestrial biodiversity should not only reduce land demand (e.g. by increasing agricultural productivity and dietary changes) but also focus on reducing or mitigating the impacts of other pressures

Characteristics of the study group, subdivided by included and excluded patients.

<p>DBD = deceased brain death, DCD = deceased cardiac death, SD = standard deviation, CsA = cyclosporine A, TAC = tacrolimus, MPA = mycophenolic acid, AZA = azathioprine, mTOR = mammalian target of rapamycin, moab = monoclonal antibody, HLA = human leukocyte antigen. HLA = Human leukocyte antigen.</p><p>¹Bonferroni corrected for multiple testing</p><p>²Data for N = 221 were missing; N = 195 (20%) in the included patients, N = 26 in the excluded (17%), <i>P</i> = 0.9.</p><p>Characteristics of the study group, subdivided by included and excluded patients.</p

Case-control study for the association between TLR single nucleotide polymorphisms and end-stage renal disease per underlying disease category.

<p>¹Per allele odds ratios (OR) and 95% confidence intervals (CI) based on additive genetic logistic regression models adjusted for age and gender, taking case-control relatedness into consideration (DFAM algorithm). HGVS = Human Genome Variation Society.</p><p>²<i>P</i>-values are Bonferroni corrected.</p><p>³<i>Post hoc</i> estimates of the type II errors (100%–power) were calculated according to the methods by Skol <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139769#pone.0139769.ref023" target="_blank">23</a>] with the data as mentioned in the table and an end-stage renal disease prevalence of 0.1% (estimate in The Netherlands).</p><p>Case-control study for the association between TLR single nucleotide polymorphisms and end-stage renal disease per underlying disease category.</p

Case-control study for the association between TLR single nucleotide polymorphsims and end-stage renal disease.

<p>¹Per allele odds ratios (OR) and 95% confidence intervals (CI) based on additive genetic logistic regression models adjusted for age and gender, taking case-control relatedness into consideration (DFAM algorithm). HGVS = Human Genome Variation Society.</p><p>²<i>P</i>-values are Bonferroni corrected.</p><p>³Estimates of the type II errors (100%–power) were calculated according to the methods by Skol <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139769#pone.0139769.ref023" target="_blank">23</a>] with the data as mentioned in the table and an end-stage renal disease prevalence of 0.1% (estimate in The Netherlands).</p><p>Case-control study for the association between TLR single nucleotide polymorphsims and end-stage renal disease.</p

Association of TLR single nucleotide polymorphism with biopsy-proven acute rejection.

<p>HR = hazard ratio (^<b>1</b>per allele combination as compared to the homozygous dominant allele combination)</p><p>CI = confidence interval, HGVS = Human Genome Variation Society. The results represent univariable crude models, i.e. no other independent variables were included.</p><p>²<i>P</i>-values are calculated by log rank tests after Bonferroni correction for multiple comparisons.</p><p>Association of TLR single nucleotide polymorphism with biopsy-proven acute rejection.</p

Association of TLR single nucleotide polymorphism with delayed graft function in univariable logistic regression analysis.

<p>OR = odds ratio (¹per allele combination as compared to the homozygous dominant allele combination)</p><p>CI = confidence interval, HGVS = Human Genome Variation Society. The results represent univariable crude models, i.e. no other independent variables were included.</p><p>²<i>P</i>-values are Bonferroni corrected.</p><p>Association of TLR single nucleotide polymorphism with delayed graft function in univariable logistic regression analysis.</p

Allele frequency distributions and possible phenotypical consequences of the single nucleotide polymorphisms in TLR-related genes.

<p>Donor and recipient genotype are displayed as dominant (A/A), heterozygous (A/a) or recessive (a/a). Chr = chromosome, HGVS = Human Genome Variation Society LOF = loss of function, GOF = gain of function, ND = not determined, MAF = minor allele frequency.</p><p>Allele frequency distributions and possible phenotypical consequences of the single nucleotide polymorphisms in TLR-related genes.</p