Implementation of a hierarchical global vegetation classification in ecosystem function models

Abstract. We propose an alternative approach for the currently used biogeographic global vegetation classifications. A hierarchical vegetation classification system is proposed for consistent and routine monitoring of global vegetation. Global vegetation is first defined into six classes based on plant canopy structure and dynamics observable by remote sensing from satellites. Additional biome variability is then represented through a remote sensing derived leaf area index map, and direct climate data sets driving an ecosystem model to compute and map net primary production and evapotranspiration. Simulation results from an ecosystem function model suggest that the six canopy structure-based classes are sufficient to represent global variability in these parameters, provided the spatio-temporal variations in Leaf Area Index and climate are characterized accurately. If a bioclimatically based classification is needed for other purposes, our six class approach can be expanded to a possible 21 classes using archived climatic zones. For example, tropical, subtropical, temperate and boreal labels are defined by absolute minimum temperature. Further separation in each class is possible through changes in water availability defined by precipitation and/or soils. The resulting vegetation classes correspond to many of the existing, conventional global vegetation schemes, yet retain the measure of actual vegetation possible because remote sensing first defines the six biome classes in our classification. Vegetation classifications are no longer an end product but a source of initializing data for global ecosystem function models. Remote sensing with biosphere models directly calculates the ecological functions previously inferred from vegetation classifications, but with higher spatial and temporal accuracy.     

Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus Nicrophorus (Coleoptera: Silphidae)

Three satellite DNA families were identified in three species of burying beetles, Nicrophorus orbicollis, N. marginatus, and N. americanus. Southern hybridization and nucleotide sequence analysis of individual randomly cloned repeats shows that these satellite DNA families are highly abundant in the genome, are composed of unique repeats, and are species-specific. The repeats do not have identifiable core elements or substructures that are similar in all three families, and most interspecific sequence similarity is confined to homopolymeric runs of A and T. Satellite DNA from N. marginatus and N. americanus show single-base-pair indels among repeats, but single-nucleotide substitutions characterize most of the repeat variability. Although the repeat units are of similar lengths (342, 350, and 354 bp) and A + T composition (65%, 71%, and 71%, respectively), the average nucleotide divergence among sequenced repeats is very low (0.18%, 1.22%, and 0.71%, respectively). Transition/transversion ratios from the consensus sequence are 0.20, 0.69, and 0.70, respectively.      

A generalized, bioclimatic index to predict foliar phenology in response to climate

The phenological state of vegetation significantly affects exchanges of heat, mass, and momentum between the Earth's surface and the atmosphere. Although current patterns can be estimated from satellites, we lack the ability to predict future trends in response to climate change. We searched the literature for a common set of variables that might be combined into an index to quantify the greenness of vegetation throughout the year. We selected as variables: daylength (photoperiod), evaporative demand (vapor pressure deficit), and suboptimal (minimum) temperatures. For each variable we set threshold limits, within which the relative phenological performance of the vegetation was assumed to vary from inactive (0) to unconstrained (1). A combined Growing Season Index (GSI) was derived as the product of the three indices. Ten‐day mean GSI values for nine widely dispersed ecosystems showed good agreement (r>0.8) with the satellite‐derived Normalized Difference Vegetation Index (NDVI). We also tested the model at a temperate deciduous forest by comparing model estimates with average field observations of leaf flush and leaf coloration. The mean absolute error of predictions at this site was 3 days for average leaf flush dates and 2 days for leaf coloration dates. Finally, we used this model to produce a global map that distinguishes major differences in regional phenological controls. The model appears sufficiently robust to reconstruct historical variation as well as to forecast future phenological responses to changing climatic conditions.     

Differential responsiveness to immunoablative therapy in refractory rheumatoid arthritis is associated with level and avidity of anti-cyclic citrullinated protein autoantibodies: a case study

In order to identify pathogenic correlates of refractory rheumatoid arthritis (RA), antibodies against anti-cyclic citrullinated protein (ACPAs) were investigated in RA patients in whom the dysregulated immune system had been ablated by high-dose chemotherapy (HDC) and autologous haematopoietic stem cell transplantation (HSCT). Six patients with refractory RA were extensively characterized in terms of levels of total immunoglobulins, RA-specific autoantibodies (ACPAs and rheumatoid factor) and antibodies against rubella, tetanus toxoid (TT) and phosphorylcholine before and after HDC plus HSCT. Additionally, the avidity of ACPAs was measured before and after treatment and compared with the avidity of TT antibodies following repeated immunizations. Synovial biopsies were obtained by arthroscopy before HDC plus HSCT, and analyzed by immunohistochemistry. In the three patients with clinically long-lasting responses to HDC plus HSCT (median 423 days), significant reductions in ACPA-IgG levels after therapy were observed (median level dropped from 215 to 34 arbitrary units/ml; P = 0.05). In contrast, stable ACPA-IgG levels were observed in three patients who relapsed shortly after HDC plus HSCT (median of 67 days). Clinical responders had ACPA-IgG of lower avidity (r = 0.75; P = 0.08) and higher degree of inflammation histologically (r = 0.73; P = 0.09). Relapse (after 38 to 530 days) in all patients was preceded by rising levels of low avidity ACPA-IgG (after 30 to 388 days), in contrast to the stable titres of high avidity TT antibodies. In conclusion, humoral autoimmune responses were differentially modulated by immunoablative therapy in patients with synovial inflammation and low avidity ACPA-IgG autoantibodies as compared with patients with high levels of high avidity ACPA-IgG. The distinct clinical disease course after immunoablative therapy based on levels and avidity of ACPA-IgG indicates that refractory RA is not a single disease entity.     

Suitable Days for Plant Growth Disappear under Projected Climate Change: Potential Human and Biotic Vulnerability

Ongoing climate change can alter conditions for plant growth, in turn affecting ecological and social systems. While there have been considerable advances in understanding the physical aspects of climate change, comprehensive analyses integrating climate, biological, and social sciences are less common. Here we use climate projections under alternative mitigation scenarios to show how changes in environmental variables that limit plant growth could impact ecosystems and people. We show that although the global mean number of days above freezing will increase by up to 7% by 2100 under “business as usual” (representative concentration pathway [RCP] 8.5), suitable growing days will actually decrease globally by up to 11% when other climatic variables that limit plant growth are considered (i.e., temperature, water availability, and solar radiation). Areas in Russia, China, and Canada are projected to gain suitable plant growing days, but the rest of the world will experience losses. Notably, tropical areas could lose up to 200 suitable plant growing days per year. These changes will impact most of the world’s terrestrial ecosystems, potentially triggering climate feedbacks. Human populations will also be affected, with up to ~2,100 million of the poorest people in the world (~30% of the world’s population) highly vulnerable to changes in the supply of plant-related goods and services. These impacts will be spatially variable, indicating regions where adaptations will be necessary. Changes in suitable plant growing days are projected to be less severe under strong and moderate mitigation scenarios (i.e., RCP 2.6 and RCP 4.5), underscoring the importance of reducing emissions to avoid such disproportionate impacts on ecosystems and people.     

Polarized light based scheme to monitor column performance in a continuous foam fractionation column

Background  

A polarized light scattering technique was used to monitor the performance of a continuously operated foam fractionation process. The S ₁₁ and S ₁₂ parameters, elements of the light scattering matrix, combined together (S ₁₁ +S ₁₂) have been correlated with the bubble size and liquid content for the case of a freely draining foam. The performance of a foam fractionation column is known to have a strong dependence on the bubble size distribution and liquid hold up in foam. In this study the enrichment is used as a metric, representative of foam properties and column performance, and correlated to the S ₁₁ +S ₁₂ parameter.     

Probing the structure of the Caulobacter crescentus ribosome with chemical labeling and mass spectrometry

The ribosomal proteins of Caulobacter crescentus were amidinated before and after disassembly of the organelle and the results analyzed by mass spectrometry. Comparison with structural information from previous X-ray crystal studies of other bacterial ribosomes provides insight about the C. crescentus ribosome. In total, 47 of the 54 proteins present in the ribosome of C. crescentus were detected after labeling. The extent of derivatization for each protein is strongly dependent on the solvent accessibility of its target residues. Proteins of the ribosome stalk, which are known to be largely solvent-accessible, were labeled quite extensively. In striking contrast, other proteins that are known to be highly shielded in their subunits were labeled at very few of their potential sites. Furthermore, evidence that protein L12 binds to the ribosome via its N-terminal domain is consistent with previous findings.