When to use what: Methods for weighting and aggregating sustainability indicators

ContextSustainability indices (SIs) have become increasingly important to sustainability research and practice. However, while the validity of SIs is heavily dependent on how their components are weighted and aggregated, the typology and applicability of the existing weighting and aggregation methods remain poorly understood.ObjectivesTo close the knowledge gap regarding when to use which weighting and aggregation methods for constructing SIs, we review the most commonly used methods for weighting and aggregating SIs, discuss their benefits and drawbacks, and suggest a process-oriented approach for choosing appropriate weighting and aggregation methods depending on research objectives.MethodsOur review synthesis was based on peer-reviewed journal articles, books, and reports by international organizations, governmental agencies, and research institutions. After carefully examining their principles, characteristics, and applications, we selected and classified the frequently used methods for indicator weighting and aggregation.ResultsWe systematically discuss the benefits and drawbacks of nine weighting methods and three aggregation methods. We propose a four-step process for choosing the most suitable weighting and aggregation methods based on: research purposes, spatial and temporal scales, and sustainability perspectives.ConclusionsIn this research, we chose the most commonly used methods for weighting and aggregating SIs and analyzed the characteristics, strengths and weaknesses of each method. We found that choosing appropriate weighting and aggregation methods for a specific sustainability assessment project is an extremely important and challenging task. To meet this challenge, we propose a process-oriented approach for properly selecting methods according to the purpose, scale and sustainability concept. This approach can facilitate the proper selection of these methods in sustainability research and practice.     

Detection of relationships among microsporidan isolates by electrophoretic analysis: hydrophobic extracts

Hydrophobic spore proteins were extracted from 11 microsporidan isolates obtained from 9 species of insects for which these microorganisms are pathogenic. Hydrophobic protein spectra were found to be stable when (1) two different genera of hosts were used for spore propagation, (2) hosts were reared at a variety of temperatures, or (3) protein was extracted from spores harvested at different stages of sporogenesis. Five consistent and distinct electrophoretic spectra were observed. Spectrum I was represented by 6 isolates including Nosema necatrix, Thelohania diazoma, Nosema plodiae, and Nosema sphingidis; spectrum II by Pleistophora sp; Spectrum III by Nosema whitei; spectrum IV by Thelohania legeri; and spectrum V by Nosema trichoplusia. The highly reproducible nature of these analyses indicated polyacrylamide gel disc electrophoresis of hydrophobic extracts can be used for the identification of Microsporida. Moreover, these analyses do not support the present classification, based mainly on the number of spores in a pansporoblast, inasfar as (1) some species of Nosema have the same pattern (I) as a species of Thelohania and (2) two species of Nosema have different patterns (III and V) in contrast to the Nosema species showing pattern I.     

Arabidopsis glutathione reductase 1 is dually targeted to peroxisomes and the cytosol

We recently established a proteome methodology for Arabidopsis leaf peroxisomes and identified more than 90 putative novel proteins of the organelle. These proteins included glutathione reductase isoform 1 (GR1), a major enzyme of the antioxidative defense system that was previously reported to be cytosolic. In this follow-up study, we validated the proteome data by analyzing the in vivo subcellular targeting of GR1 and the function of its C-terminal tripeptide, TNL>, as a putative novel peroxisome targeting signal type 1 (PTS1). The full-length protein was targeted to peroxisomes in onion epidermal cells when fused N-terminally with the reporter protein. The efficiency of peroxisome targeting, however, was weak upon expression from a strong promoter, consistent with the idea that the enzyme is dually targeted to peroxisomes and the cytosol in vivo. The reporter protein that was extended C-terminally by 10 amino acid residues of GR1 was directed to peroxisomes, characterizing TNL> as a novel PTS1. The data thus identify plant peroxisomal GR at the molecular level in the first plant species and complete the plant peroxisomal ascorbate-glutathione cycle. Moreover, GR1 is the first plant protein that is dually targeted to peroxisomes and the cytosol. The evolutionary origin and regulatory mechanisms of dual targeting are discussed.Key words: ascorbate-glutathione cycle, dual targeting, proteome analyses, reactive oxygen species, targeting signalsMassive amounts of hydrogen peroxide (H₂O₂) are produced during photosynthesis in peroxisomes by glycolate oxidase activity as part of the photorespiratory cycle.¹ Next to catalase, the ascorbate-glutathione cycle is the secondary scavenging system for H₂O₂ detoxification.^2–4 The cycle comprises four enzymes, ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR), dehydroascorbate reductase (DHAR) and NADPH-dependent glutathione reductase (GR). GR plays a major physiological role in maintaining and regenerating reduced glutathione in response to biotic and abiotic stresses in plants.⁵ Jiminez et al. (1997) provided biochemical evidence for the presence of the antioxidants ascorbate and glutathione and the enzymes of the ascorbate-glutathione cycle in pea peroxisomes.^6–8 While Arabidopsis APX3, MDAR1 and MDAR4 have been characterized as peroxisomal isoforms,^9–11 the molecular identity of plant peroxisomal GR and DHAR have not been determined in any plant species to date.⁵ Arabidopsis encodes two GR and five DHAR isoforms that are either shown to be or predicted to be cytosolic, mitochondrial or plastidic.¹² We recently identified specific isoforms of GR (GR1, At3g24170) and DHAR (DHAR1, At1g19570) as being peroxisome-associated by proteome analysis of Arabidopsis leaf peroxisomes.^13,14 Both isoforms were previously reported to be or predicted to be cytosolic.¹⁵Arabidopsis GR1 terminates with TNL>, which is related to functional plant PTS1 tripeptides such as SNL> and ANL>.^16,17 Threonine (T), however, has not yet been described as an allowed residue at position −3 of PTS1s in any plant peroxisomal protein.¹⁶ Analysis of homologous plant proteins and expressed sequence tags (ESTs) shows that TNL> is generally highly conserved in putative plant GR1 orthologs (Fig. 1). A few other sequences terminate with related tripeptides, such TSL>, TTL>, NNL> and TKL>. Only a single EST (Picrorhiza kurrooa) carries the canonical PTS1, SKI> (Fig. 1). The data provide only weak additional support for peroxisome targeting of plant GR1 orthologs. However, GR homologs from green algae (chlorophyta) carry canonical PTS1 tripeptides, such as SKL> (Chlamydomonas, Volvox) and AKM> (Micromonas, Fig. 1, Suppl. Fig. 1).Open in a separate windowFigure 1Analysis of PTS1 conservation in plant GR1 homologs. Sequences of full-length protein (FLP) plant GR1 homologs or ESTs (“EST”) were identified by BLAST and phylogenetic analysis, aligned by ClustalX, and conserved residues were shaded by Genedoc. In addition to spermatophyta, homologs from bryophyta and chlorophyta were analyzed for PTS1 conservation. For a phylogenetic analysis of the full-length proteins, see also Supplementary Figure 1. The species abbreviations are as follows: Aa, Artemisia annua; At, Arabidopsis thaliana; Bn, Brassica napus; Br, Brassica rapa; Ci, Cichorium intybus; Cr, Chlamydomonas reinhardtii; Cs, Cynara scolymus; Fv, Fragaria vesca; Ha, Helianthus annuus; Msp, Micromonas sp. RCC 299; Mt, Medicago truncatula; Nt, Nicotiana tabacum; Os, Oryza sativa; Pk, Picrorhiza kurrooa; Ppat, Physcomitrella patens subsp. patens; Ps, Pisum sativum; Ptri, Populus trichocarpa; Rc, Ricinus communis; Rs, Raphanus sativus; Tp, Trifolium pratense; Tpus, Triphysaria pusilla; Vc, Volvox carteri f. nagariensis; Vv, Vitis vinifera; Zm, Zea mays.     

Head-to-head comparison of the safety of tocilizumab and tumor necrosis factor inhibitors in rheumatoid arthritis patients (RA) in clinical practice: results from the registry of Japanese RA patients on biologics for long-term safety (REAL) registry

IntroductionThe objective of this study was to directly compare the safety of tocilizumab (TCZ) and TNF inhibitors (TNFIs) in rheumatoid arthritis (RA) patients in clinical practice.MethodsThis prospective cohort study included RA patients starting TCZ [TCZ group, n = 302, 224.68 patient-years (PY)] or TNFIs [TNFI group, n = 304, 231.01 PY] from 2008 to 2011 in the registry of Japanese RA patients on biologics for long-term safety registry. We assessed types and incidence rates (IRs) of serious adverse events (SAEs) and serious infections (SIs) during the first year of treatment. Risks of the biologics for SAEs or SIs were calculated using the Cox regression hazard analysis.ResultsPatients in the TCZ group had longer disease duration (P <0.001), higher disease activity (P = 0.019) and more frequently used concomitant corticosteroids (P <0.001) than those in the TNFI group. The crude IR (/100 PY) of SIs [TCZ 10.68 vs. TNFI 3.03; IR ratio (95% confidence interval [CI]), 3.53 (1.52 to 8.18)], but not SAEs [21.36 vs. 14.72; 1.45 (0.94 to 2.25)], was significantly higher in the TCZ group compared with the TNFI group. However, after adjusting for covariates using the Cox regression hazard analysis, treatment with TCZ was not associated with higher risk for SAEs [hazard ratio (HR) 1.28, 95% CI 0.75 to 2.19] or SIs (HR 2.23, 95% CI 0.93 to 5.37).ConclusionsThe adjusted risks for SAEs and SIs were not significantly different between TCZ and TNFIs, indicating an influence of clinical characteristics of the patients on the safety profile of the biologics in clinical practice.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0583-8) contains supplementary material, which is available to authorized users.     

The Octatricopeptide Repeat Protein Raa8 Is Required for Chloroplast trans Splicing

The mRNA maturation of the tripartite chloroplast psaA gene from the green alga Chlamydomonas reinhardtii depends on various nucleus-encoded factors that participate in trans splicing of two group II introns. Recently, a multiprotein complex was identified that is involved in processing the psaA precursor mRNA. Using coupled tandem affinity purification (TAP) and mass spectrometry analyses with the trans-splicing factor Raa4 as a bait protein, we recently identified a multisubunit ribonucleoprotein (RNP) complex comprising the previously characterized trans-splicing factors Raa1, Raa3, Raa4, and Rat2 plus novel components. Raa1 and Rat2 share a structural motif, an octatricopeptide repeat (OPR), that presumably functions as an RNA interaction module. Two of the novel RNP complex components also exhibit a predicted OPR motif and were therefore considered potential trans-splicing factors. In this study, we selected bacterial artificial chromosome (BAC) clones encoding these OPR proteins and conducted functional complementation assays using previously generated trans-splicing mutants. Our assay revealed that the trans-splicing defect of mutant F19 was restored by a new factor we named RAA8; molecular characterization of complemented strains verified that Raa8 participates in splicing of the first psaA group II intron. Three of six OPR motifs are located in the C-terminal end of Raa8, which was shown to be essential for restoring psaA mRNA trans splicing. Our results support the important role played by OPR proteins in chloroplast RNA metabolism and also demonstrate that combining TAP and mass spectrometry with functional complementation studies represents a vigorous tool for identifying trans-splicing factors.     

Microbial sucrose isomerases: producing organisms, genes and enzymes

Sucrose isomerase (SI) activity is used industrially for the conversion of sucrose into isomers, particularly isomaltulose or trehalulose, which have properties advantageous over sucrose for some food uses. All of the known microbial SIs are TIM barrel proteins that convert sucrose without need for any cofactors, with varying kinetics and product specificities. The current analysis was undertaken to bridge key gaps between the information in patents and scientific publications about the microbes and enzymes useful for sucrose isomer production.This analysis shows that microbial SIs can be considered in 5 structural classes with corresponding functional distinctions that broadly align with the taxonomic differences between producing organisms. The most widely used bacterial strain for industrial production of isomaltulose, widely referred to as “Protaminobacter rubrum” CBS 574.77, is identified as Serratia plymuthica. The strain producing the most structurally divergent SI, with a high product specificity for trehalulose, widely referred to as “Pseudomonas mesoacidophila” MX-45, is identified as Rhizobium sp.Each tested SI-producer is shown to have a single SI gene and enzyme, so the properties reported previously for the isolated proteins can reasonably be associated with the products of the genes subsequently cloned from the same isolates and SI classes. Some natural isolates with potent SI activity do not catabolize the isomer under usual production conditions. The results indicate that their industrial potential may be further enhanced by selection for variants that do not catabolize the sucrose substrate.     

Recent advances in genes involved in secondary metabolite synthesis,hyphal development,energy metabolism and pathogenicity in Fusarium graminearum (teleomorph Gibberella zeae)

The ascomycete fungus, Fusarium graminearum (teleomorph Gibberella zeae), is the most common causal agent of Fusarium head blight (FHB), a devastating disease for cereal crops worldwide. F. graminearum produces ascospores (sexual spores) and conidia (asexual spores), which can serve as disease inocula of FHB. Meanwhile, Fusarium-infected grains are often contaminated with mycotoxins such as trichothecenes (TRIs), fumonisins, and zearalenones, among which TRIs are related to the pathogenicity of F. graminearum, and these toxins are hazardous to humans and livestock. In recent years, with the complete genome sequencing of F. graminearum, an increasing number of functional genes involved in the production of secondary metabolites, hyphal differentiation, sexual and asexual reproduction, virulence and pathogenicity have been identified from F. graminearum. In this review, the secondary metabolite synthesis, hyphal development and pathogenicity related genes in F. graminearum were thoroughly summarized, and the genes associated with secondary metabolites, sexual reproduction, energy metabolism, and pathogenicity were highlighted.     

Morphology of Hydrozetes confervae () and H. parisiensis (Acari: Oribatida: Hydrozetidae), and keys to European species of Hydrozetes Berlese, 1902

Hydrozetes confervae [Schrank, F.P., 1781. Enumeratio insectorum Austriae indigenorum. Augustae Vindeliciorum, 1-552] and Hydrozetes parisiensis [Grandjean, F., 1948. Sur les Hydrozetes (Acariens) de l’Europe occidentale. Bull. Mus. Nat. Hist. nat., Paris, ser. 2(20), 328-335] are common European species of the aquatic oribatid mite family Hydrozetidae, but their external morphology is incompletely known. We describe and illustrate their larvae for the first time, and the nymphs of both species are redescribed and illustrated. Juveniles of the two species differ mainly by the position of gastronotal seta lm in relation to the opisthonotal gland opening (gla) and by the number of extremely long posterior hysterosomal setae in nymphs. In H. confervae seta lm inserts anteromedial to gla, but posterior to gla in H. parisiensis; nymphs of H. confervae have three pairs of long hysterosomal setae, while H. parisiensis has a larger, but variable number. Separate identification keys for the larvae, nymphs and adults of all known European species of Hydrozetes Berlese, 1902, are presented.     

The effect of toxin-producing Fusarium fungi on behavior of the rice weevil Sitophilus oryzae (Coleoptera,Dryophthoridae)

The paper describes laboratory tests in which the behavior response of adult rice weevils Sitophilus oryzae L. to the presence of seven species of micromycetes of the genus Fusarium (F. graminearum, F. culmorum, F. cerealis, F. poae, F. sporotrichioides, F. langsethiae, and F. sibiricum; 3 strains for each species) infecting cereals was characterized. The chemicals of unkown structure, released by the fungi, can have both attractive and repellent effects on the weevils; in some cases a neutral response was observed. The strains of Fusarium species characterized as weak pathogens (F. langsethiae, F. poae, and F. sibiricum) in most cases stimulated attractive and neutral responses. Relatively strong pathogens (F. cerealis, F. culmorum, F. graminearum, and F. sporotrichioides) generally had a repellent effect. The results obtained are discussed in the context of possible relationships between Fusarium fungi and the rice weevil during their utilization of cereals as a shared food substrate.     

A Multilocus Phylogeny of the World Sycoecinae Fig Wasps (Chalcidoidea: Pteromalidae)

The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades. All topologies estimated using maximum likelihood and Bayesian methods were similar and well resolved but did not support the existing classification. A high degree of morphological convergence was highlighted and several species appeared best described as species complexes. We therefore proposed a new classification for the subfamily. Our analyses revealed several cases of probable speciation on the same host trees (up to 8 closely related species on one single tree of F. sumatrana), which raises the question of how resource partitioning occurs to avoid competitive exclusion. Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history. Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.     

Quantification of Siderophore and Hemolysin from Stachybotrys chartarum Strains, Including a Strain Isolated from the Lung of a Child with Pulmonary Hemorrhage and Hemosiderosis

A strain of Stachybotrys chartarum was recently isolated from the lung of a pulmonary hemorrhage and hemosiderosis (PH) patient in Texas (designated the Houston strain). This is the first time that S. chartarum has been isolated from the lung of a PH patient. In this study, the Houston strain and 10 strains of S. chartarum isolated from case (n = 5) or control (n = 5) homes in Cleveland were analyzed for hemolytic activity, siderophore production, and relatedness as measured by random amplified polymorphic DNA analysis.     

Can synchronizing feather-based measures of corticosterone and stable isotopes help us better understand habitat–physiology relationships?

Physiological mechanisms link the environment with population dynamics, and glucocorticoid hormones are of particular interest because they respond adaptively to environmental change and can influence vertebrate reproduction and fitness. We tested a novel approach of synchronizing feather-based measures of corticosterone (the primary avian glucocorticoid; CORT_f) and ratios of stable isotopes (SIs) of C (δ¹³C) and N (δ¹⁵N) to provide information about environmental conditions and an integrated physiological response to those conditions over the same period of feather synthesis. Using a fragmented metapopulation of Dupont’s larks Chersophilus duponti, an endangered steppe songbird, we analyzed interrelationships among CORT_f, δ¹³C, δ¹⁵N, and the physical environment, including measures of habitat loss and fragmentation. CORT_f was not related to any habitat variable measured directly. However, we detected a significant spatial structure to CORT_f values and food availability, with greater similarity in both at smaller spatial scales. Using SIs as proxies for the local environment, we found CORT_f was negatively related to δ¹³C. Values of CORT_f, δ¹³C, and the relationship between the two were likely driven by variation in agricultural land use surrounding lark habitat patches. Our feather-based approach revealed that individual physiology was sensitive to environmental conditions (e.g., an interaction of food availability and variation in habitat) at a local scale, but not patch or landscape scales. Combining CORT_f and SIs may be a promising tool because it can provide individual-based information about habitat, physiology, and their relationship during the same time period.     

F factor mobilization of non-conjugative chimeric plasmids in Escherichia coli: General mechanisms and a role for site-specific recA-independent recombination at oriV1

Plasmid pSC101 is neither self-transmissible nor efficiently mobilized (made to transfer) by the Escherichia coli F factor. When fragments of F factor DNA were inserted into pSC101 the resulting chimeric plasmids were mobilized by the F factor at enhanced frequencies. These chimeric plasmids, which were not self-transmissible, fell into three classes according to their relative ability to be mobilized by an autonomous or integrated F factor: (1) class I pSC101-F chimeric plasmids contain the origin of transfer of the F factor (oriT) and were mobilized in trans at an efficiency nearly equal to that of F factor transfer; (2) class II pSC101-F chimeric plasmids lacked both oriT and the origin of vegetative F replication (oriV1), and were mobilized in cis via fusion with the F factor in a recA-dependent recombination to yield a transferable co-integrated plasmid; (3) class III pSC101-F chimeric plasmids lacked oriT but contained oriV1 and were mobilized in cis via co-integration with the F factor probably at oriV1 in a recA-independent recombination. A fourth class of mobilization event, not exhibited by pSC101-F chimeric plasmids, was also observed. Mobilization of pBR322 and pSC101 occurred in cis via transposon-mediated recA-independent fusion with F. On the basis of these results we present a general classification scheme of non-conjugative plasmids and also suggest mechanisms for their mobilization.     

Survival of Aspergillus flavus and Fusarium moniliforme in High-Moisture Corn Stored Under Modified Atmospheres

Freshly harvested high-moisture corn with 29.4% moisture and corn remoistened to 19.6% moisture were inoculated with Aspergillus flavus Link ex Fr. and stored for 4 weeks at about 27 C in air (0.03% CO₂, 21% O₂, and 78% N₂) and three modified atmospheres: (i) 99.7% N₂ and 0.3% O₂; (ii) 61.7% CO₂, 8.7% O₂, and 29.6% N₂; and (iii) 13.5% CO₂, 0.5% O₂, and 84.8% N₂. Kernel infections by A. flavus, Fusarium moniliforme (Sheld.) Snyd. et Hans., and other fungi were monitored weekly. The modified-atmosphere treatments delayed deterioration by A. flavus and F. moniliforme, but their growth was not completely stopped. A. flavus survived better in the remoistened than in the freshly harvested corn. F. moniliforme survived in both. A. flavus and F. moniliforme were the dominant fungi in corn removed from the modified atmospheres and exposed to normal air for 1 week.