Possibility Theory: A New Approach to Uncertainty Analysis? (3 pp)

Background, Aims and Scope The problem of the evaluation of practitioner's belief and belief-related uncertainties on LCA results obtained from different methodological choices has been addressed so far by scenario modeling, Cultural Theory perspectives and probabilistic simulation. The direct evaluation of belief and related uncertainties could be of interest, e.g. when the information available (resulting from classical uncertainty analysis or the application of the precautionary principle) do not allow one to choose between methodological alternatives leading to different LCA results and conclusions. The difficulty of modeling belief arises from the additive nature of classical measures, e.g. probabilities. Since the 1960s, non-additive measures (e.g. possibilities) have been developed and applied to model belief in real world problems. The aim of this paper is to discuss the application of possibility measures in LCA for uncertainty analysis in complement to classical approaches. Methods The nature and the meaning of possibilities are briefly introduced by comparison with probabilities (subjective or not) in order to enlighten strengths, drawbacks and complementarities. A tentative possibilistic approach based on the evaluation of a posteriori possibilities of final LCA results depending on a priori possibilities of the methodological choices behind the calculations is described, also by means of an application example. Results and Outlook. A new approach for the modeling of practitioner's belief and belief-related uncertainties in complement of classical methods of uncertainty analysis has been proposed for discussion. Uncertainty can be characterized by confidence intervals and indexes that could help practitioners in making methodological choices and could improve the interpretation and reliability of LCA results, still increasing its sophistication.     

A New Approach to the Synthesis of Isoflavones, 2′-Hydroxyisoflavones and an Alternative Synthesis of (±)-Pterocarpin

A new approach to the synthesis of isoflavones and 2′-hydroxyisoflavones, useful intermediates for synthesis of pterocarpinoids, are described. The 2′-hydroxyisoflavone (VIII; R=CH₃, R′=H) synthesized by this method, was converted into (±)-pterocarpin (VII; R=CH₃, R′=H). Attempts to obtain the corresponding isoflavane or isoflavene from the coumarine (XVII) failed.     

How sensitive are climatic niche inferences to distribution data sampling? A comparison of Biota of North America Program (BONAP) and Global Biodiversity Information Facility (GBIF) datasets

Climatic niche modeling is widely used in modern macroecology and evolutionary biology to model species' distributions and ecological niches. Frequently, Global Biodiversity Information Facility (GBIF) distribution data are used as raw data for such models. Unfortunately, the accuracy of resulting niche estimates is difficult to assess, and GBIF users continue to call for a better understanding of GBIF data precision and uncertainty. Our research evaluates how GBIF data perform in comparison with curated, county-level species distributions from the Biota of North America Program (BONAP; www.bonap.org) to estimate the climatic niche for Carex (Cyperaceae), one of the largest angiosperm genera in the temperate zone. In particular, we investigate the complementary strengths and weaknesses of the two datasets in the context of climatic niche estimation, namely (1) the incomplete sampling coverage of species distributions of GBIF data, and (2) elevation bias in climatic niche estimates resulting from the coarse resolution of the BONAP distribution dataset. To do so, we quantified climatic niches for 388 North American Carex species and calculated the distance of GBIF and BONAP climatic niche estimates in principal component space. We found little to no relationship between differences in climatic niche estimates and sampling coverage metrics, suggesting that sparse sampling coverage of GBIF data may have negligible average effects on mean climate estimates at the species level. However, elevation had a significant effect on differences in niche estimates, suggesting that using county-level distribution data—in our study, represented by BONAP—may introduce a bias in estimated climatic niche. To investigate if any such bias is phylogenetically structured, we examined the relationship between GBIF and BONAP climatic niche tip states using Phylogenetic Generalized Least Squares Regression (PGLS), estimating phylogenetic signal in the residuals of the regression by estimating Pagel's λ simultaneously with other regression parameters. Estimates were tightly correlated, with little to no phylogenetic signal—low λ—in the regression residuals, suggesting that any potential bias is more or less independent of phylogeny for the sedges of North America. Based on our results, we recommend a hybrid GBIF and BONAP data approach for the best understanding of species' climatic niche, relying on BONAP to fill in distributions primarily where collection records may be sparse. Our findings provide needed context and perspective on the implications of alternative distribution datasets for climatic niche estimation, especially in a macroevolutionary context.     

The Modes of Binding Methyl—α (and β)-D-glucopyranosides and Some of their Derivatives to Concanavalin A—A Theoretical Approach

Abstract

The probable modes of binding of Methyl—α (and β)-D-glucopyranosides and some of their derivatives to concanavalin A have been proposed from theoretical studies. Theory predicts that βMeGlcP can bind to ConA in three different modes whereas α-MeGlcP can bind only in one mode. βMeGlcP in its most favourable mode of binding differs from α-MeGlcP in its alignment in the active-site of the lectin where it binds in a flipped or inverted orientation. Methyl substitution at the C-2 atom of the α-MeGlcP does not significantly affect the possible orientations of the sugar in the active-site of the lectin. Methyl substitution at C-3 or C-4, however, affects the allowed orientations drastically leading to the poor inhibiting power of Methyl-3-O-methyl-α-D-glucopyranoside and the inactivity of Methyl-4-O-methyl-α-D-glucopyranoside. These studies suggest that the increased activity of the α-MeGlcP over β-MeGlcP may be due to the possibility of formation of better hydrogen bonds and to hydrophobic interactions rather than to steric factors as suggested by earlier workers. These models explain the available NMR and other binding studies.     

Measuring Hordein (Gluten) in Beer – A Comparison of ELISA and Mass Spectrometry

Background

Subjects suffering from coeliac disease, gluten allergy/intolerance must adopt a lifelong avoidance of gluten. Beer contains trace levels of hordeins (gluten) which are too high to be safely consumed by most coeliacs. Accurate measurement of trace hordeins by ELISA is problematic.

Methods

We have compared hordein levels in sixty beers, by sandwich ELISA, with the level determined using multiple reaction monitoring mass spectrometry (MRM-MS).

Results

Hordein levels measured by ELISA varied by four orders of magnitude, from zero (for known gluten-free beers) to 47,000 µg/mL (ppm; for a wheat-based beer). Half the commercial gluten-free beers were free of hordein by MS and ELISA. Two gluten-free and two low-gluten beers had zero ELISA readings, but contained significant hordein levels (p<0.05), or near average (60–140%) hordein levels, by MS, respectively. Six beers gave false negatives, with zero ELISA readings but near average hordein content by MS. Approximately 20% of commercial beers had ELISA readings less than 1 ppm, but a near average hordein content by MS. Several barley beers also contained undeclared wheat proteins.

Conclusions

ELISA results did not correlate with the relative content of hordein peptides determined by MS, with all barley based beers containing hordein. We suggest that mass spectrometry is more reliable than ELISA, as ELISA enumerates only the concentration of particular amino-acid epitopes; this may vary between different hordeins and may not be related to the absolute hordein concentration. MS quantification is undertaken using peptides that are specific and unique, enabling the quantification of individual hordein isoforms. This outlines the problem of relying solely on ELISA determination of gluten in beverages such as beer and highlights the need for the development of new sensitive and selective quantitative assay such as MS.     

Protective Role of α-tocopherol-succinate (Provitamin-E) in Cyclophosphamide Induced Testicular Gametogenic and Steroidogenic Disorders: A Correlative Approach to Oxidative Stress

The present study was undertaken to find out the adverse effects of cyclophosphamide on testicular activities along with testicular oxidative stress at its therapeutic dose and the protective effects of &#102 -tocopherol succinate on testicular dysfunctions induced by cyclophosphamide in mature albino rats. A significant diminution in the activities of testicular &#106 5 , 3 &#103 -hydroxysteroid dehydrogenase (HSD) and 17 &#103 -hydroxysteroid dehydrogenase (HSD) along with significant reduction in the plasma level of testosterone and number of spermatogonia-A (ASg), preleptotene spermatocytes (pLSc), midpachytene spermatocytes (mPSc) and step 7 spermatids (7Sd) at stage VII of spermatogenic cycle were observed following cyclophosphamide treatment. Oxidative stress was also noted in testis, which was enlightened by significant elevation in the level of malondialdehyde (MDA) and conjugated dienes along with significant reduction in the activities of testicular peroxidase and catalase. Co-administration of &#102 -tocopherol succinate in cyclophosphamide-treated rats resulted a significant restoration of all the above-mentioned parameters to the control level. The results of our experiment suggest that cyclophosphamide treatment at its clinical dose is associated with antigonadal activities as well as induction of oxidative stress in gonad that can be ameliorated significantly by &#102 -tocopherol succinate co-administration. So, our data have some potential clinical implications.     

Diversity in Guanosine 3′,5′-Bisdiphosphate (ppGpp) Sensitivity among Guanylate Kinases of Bacteria and Plants

The guanosine 3′,5′-bisdiphosphate (ppGpp) signaling system is shared by bacteria and plant chloroplasts, but its role in plants has remained unclear. Here we show that guanylate kinase (GK), a key enzyme in guanine nucleotide biosynthesis that catalyzes the conversion of GMP to GDP, is a target of regulation by ppGpp in chloroplasts of rice, pea, and Arabidopsis. Plants have two distinct types of GK that are localized to organelles (GKpm) or to the cytosol (GKc), with both enzymes being essential for growth and development. We found that the activity of rice GKpm in vitro was inhibited by ppGpp with a K_i of 2.8 μm relative to the substrate GMP, whereas the K_m of this enzyme for GMP was 73 μm. The IC₅₀ of ppGpp for GKpm was ∼10 μm. In contrast, the activity of rice GKc was insensitive to ppGpp, as was that of GK from bakers'' yeast, which is also a cytosolic enzyme. These observations suggest that ppGpp plays a pivotal role in the regulation of GTP biosynthesis in chloroplasts through specific inhibition of GKpm activity, with the regulation of GTP biosynthesis in chloroplasts thus being independent of that in the cytosol. We also found that GKs of Escherichia coli and Synechococcus elongatus PCC 7942 are insensitive to ppGpp, in contrast to the ppGpp sensitivity of the Bacillus subtilis enzyme. Our biochemical characterization of GK enzymes has thus revealed a novel target of ppGpp in chloroplasts and has uncovered diversity among bacterial GKs with regard to regulation by ppGpp.     

Diversity,dynamic and ecology of freshwater snails related to environmental factors in urban and suburban streams in Douala–Cameroon (Central Africa)

Urban land use has increased dramatically over the past few decades, resulting in high variability in nutrients loading which is likely to alter the biological component of urban streams. Freshwater snails and environmental variables that might structure their diversity and distribution were studied from September 2012 to September 2013 in three contiguous watersheds in Douala. Twelve stations were monitored monthly, two of these are located in a suburban forest area, and the rest situated in urbanized and industrialized zones. Snails were collected using a long-handled net (30 × 30 cm side, 400-µm mesh). Meanwhile, measurements of the environmental variables were taken. Ten species were recorded which are as follows: Melanoides tuberculata (Thiaridae); Gabbiella africana (Bythiniidae); Physa acuta, Aplexa sp. (Physidae); Lymnaea natalensis, Lymnaea stagnalis, Lymnaea columella (Lymnaeidae); Biomphalaria pfeifferi, Bulinus forskalii (Planorbidae) and one undetermined taxon of Bythiniidae. All these snails were identified at nine of the ten urban stations; no species being found in suburban stations. These urban streams have very poor health status with highly polluted waters. Among the species found P. acuta (76.95 %), L. natalensis (19.46 %) and M. tuberculata (2.79 %) were the most abundant. Multiple stepwise regression analysis, Spearman correlation test and redundancy analysis showed that snail occurrences and abundances were probably influenced by water temperature, conductivity, suspended solids, alkalinity, nitrites, nitrates, ammonium, phosphates, oxydability, biochemical oxygen demand, rainfall, encumbrance rate of the riverbed and water width. Moreover, snail dynamics showed a seasonal pattern with peak population abundances and recruitment of young generations during rainy season. This malacological survey spotlighted the impacts of anthropogenic activities on snail’s diversity and distribution, with the proliferation of the invasive pulmonate P. acuta in Douala urban streams.     

Use of Spin Traps in Intact Animals Undergoing Myocardial Ischemia/Reperfusion: A New Approach to Assessing the Role of Oxygen Radicals in Myocardial “Stunning”

Numerous studies have indirectly, suggested that oxygen-derived free radicals play an important path-ogenetic role in the prolonged depression of contractile function observed in myocardium reperfused after reversible ischemia (myocardial “stunning”). In order to provide direct evidence for the oxy-radical hypothesis of stunning, we administered the spin trap, α-phenyl N-tert-butyl nitrone (PBN), to open-chest dogs undergoing a 15-min coronary artery occlusion followed by reperfusion. Plasma of local coronary venous blood was analyzed by electron paramagnetic resonance (EPR) spectroscopy. EPR signals characteristic of radical adducts of PBN appeared during ischemia and increased dramatically in the first few minutes after reperfusion. After this initial burst, the production of adducts abated but did not cease, persisting up to 3 h after reflow. The production of PBN adducts after reperfusion was inversely related to collateral flow during ischemia. PBN itself enhanced recovery of contractile function. indicating that the radicals trapped may play a pathogenetic role in myocardial stunning. Superoxide dismutase plus catalase attenuated PBN adduct production and, at the same time, improved recovery of contractile function. Antioxidant therapy given 1 min before reperfusion suppressed PBN adduct production and improved contractile recovery; however, the same therapy given 1 min after reperfusion did not suppress early radical production and did not attenuate contractile dysfunction. After i.v. administration, the elimination half-life of PBN was estimated to be approximately 4–5 h. The results demonstrate that 1) free radicals are produced in the stunned myocardium in intact animals; 2) inhibition of free radical production results in improved contractile recovery; and 3) the free radicals important in causing dysfunction are produced in the first few minutes of reperfusion. Taken together, these studies provide cogent evidence supporting the oxy-radical hypothesis of stunning in open-chest dogs. It is now critical to determine whether these results can be reproduced in conscious animal preparations.     

N-cadherin knockdown leads to disruption of trophoblastic and endothelial cell interaction in a 3D cell culture model – New insights in trophoblast invasion failure

Introduction: Trophoblast homing to maternal spiral arteries is mandatory for successful placentation. Cell-cell adhesion molecules regulate this process and adhesion molecule expression is altered in impaired placentation. We hypothesize that, similar to immune cell recruitment, trophoblast cell adherence and rolling are primarily mediated by adhesion molecules like, cadherins, immunoglobulins, selectins and their partnering ligands. Here, the interdependence of adhesion molecule expression in trophoblastic cell lines of diverse origin was investigated in relation to their interaction with endothelial cell networks on Matrigel® co-cultures and the effect of specific adhesion molecule knockdown analyzed. Methods: Trophoblastic cells were labeled in red and co-cultured with green HUVEC networks on Matrigel®. Association was quantified after collection of fluorescence microscopy pictures using Wimasis® internet platform and software. Expression of adhesion molecules was analyzed by PCR and Western blot, immuno-fluorescence and flow cytometry. The impact of adhesion molecules on trophoblast-endothelial-cell interaction was investigated using siRNA technique. Results: N-cadherin and CD162 were specifically expressed in the trophoblast cell line HTR-8/SVneo, which closely adhere to and actively migrate toward HUVEC networks on Matrigel®. Suppression of N-cadherin led to a significant alteration in trophoblast-endothelial cell interaction. Expression of VE-cadherin in closely interacting trophoblast cells was not confirmed in vitro. Discussion: We identified N-cadherin to mediate specific interaction between HUVEC and the migrating trophoblast cells HTR-8/SVneo in a Matrigel® co-culture model. VE-cadherin contribution could not be confirmed in vitro. Our results support the hypothesis that impaired N-cadherin but not VE-cadherin expression is involved in trophoblast recruitment to the maternal endothelium.     

Ecological Flexibility in Boutourlini’s Blue Monkeys (Cercopithecus mitis boutourlinii) in Jibat Forest, Ethiopia: A Comparison of Habitat Use, Ranging Behavior, and Diet in Intact and Fragmented Forest

Comparisons of the behavior and ecology of primates living in intact and fragmented forest are critical to the development of conservation strategies for the many primate taxa threatened by habitat loss. From July 2009 to April 2010, we investigated the habitat use, ranging behavior, and diet of two groups of Boutourlini’s blue monkeys (Cercopithecus mitis boutourlinii), a subspecies endemic to western Ethiopia, whose habitats had experienced different levels of disturbance at Jibat Forest. Forest Group occupied primarily continuous tree-dominated forest with little human disturbance whereas Fragment Group inhabited a heavily degraded 2- to 3-km² forest fragment nearly surrounded by farmland and connected tenuously to the continuous forest by a narrow corridor of riverine forest. Mean daily path lengths for both groups were nearly identical (Forest Group: 799 m; Fragment Group: 783 m) and exhibited little seasonal variability. The mean home range areas of Forest Group and Fragment Group were 72.0 and 61.2 ha, respectively. Forest Group (N?=?2232 feeding records) fed mostly on fruits (52.5 %), though they also ate animal prey (14.7 %), young leaves (11.1 %), shoots (8.7 %), and flowers (7.3 %). In contrast, fruits accounted for only 17.0 % of Fragment Group’s diet (N?=?2903 feeding records), with shoots (29.8 %), young leaves (17.1 %), animal prey (13.1 %), seeds (9.6 %), and flowers (6.8 %) also making substantial contributions to their diet. Only Fragment Group engaged in crop raiding, consuming seeds from barley and wheat extensively (33–41 % of diet) during 2 mo. Fragment Group (N?=?33) ate more plant species than Forest Group (N?=?24), though both groups exploited a small number of plant species relative to other subspecies of blue monkeys. Our study revealed that, like most other blue monkey subspecies, Boutourlini’s blue monkeys are quite flexible in the habitats they occupy as well as in their foraging habits. Despite this ecological flexibility, the long-term conservation of Boutourlini’s blue monkey is far from assured given its limited distribution, the rapidly growing human population, and the high rates of forest clearance in western Ethiopia.     

Biodiversity and endemism mapping as a tool for regional conservation planning – case study of the Pleurothallidinae (Orchidaceae) of the Andean rain forests in Bolivia

Analyses of species diversity and endemism patterns provide vital inputs for conservation planning. Therefore, it is an important dilemma of biodiversity conservation that in very diverse but poorly studied tropical countries those patterns can hardly be considered. Consequently, there is an urgent need to develop prediction models that make the best use of existing data on species distribution and that can give hints on spatial conservation priorities. This paper presents the results of a pilot study on the diversity of the orchid subtribe Pleurothallidinae (331 mapped species) in the Andean rain forests of Bolivia. Results of a taxon-based mapping methodology, using abiotic (humidity and temperature, the latter indicated by altitude) and historical factors (taken into account as distance from collection localities) that determine species ranges, are compared with outcomes of an inventory-based mapping approach. The patterns of taxon-based diversity and endemism show a strong correlation with the distribution of sample localities. The inventory-based approach is more reliable, but it is interesting to apply both mapping methods in order to make a critical interpretation and comparison that facilitates some valuable conservation recommendations. We end with concrete conclusions for conservation planning and action.     

Mapping and genomic characterization of the gene encoding diacylglycerol kinase γ (DAGK3): assessment of its role in dominant optic atrophy (OPA1)

The family of diacylglycerol kinases (DAGKs) is known to play an important role in signal transduction linked to phospholipid turnover. In the fruitfly Drosophila melanogaster, a human DAGK ortholog, DGK2, was shown to underlie the phenotype of the visual mutant retinal degeneration A (rdgA). Previously, the gene encoding a novel member of the human DAGK family, termed DAGK3, was cloned and demonstrated to be abundantly expressed in the human retina. Based on these findings we reasoned that DAGK3 might be an excellent candidate gene for a human eye disease. In the present study, we report the genomic organization of the human DAGK3 gene, which spans over 30 kb of genomic DNA interrupted by 23 introns. In addition, we have mapped the gene locus by fluorescence in situ hybridization to 3q27–28, overlapping the chromosomal region known to contain the gene underlying dominant optic atrophy (OPA1), the most common form of hereditary atrophy of the optic nerve. Mutational analysis of the entire coding region of DAGK3 in 19 unrelated German OPA1 patients has not revealed any disease-causing mutations, therefore excluding DAGK3 as a major cause underlying OPA1. Received: 24 August 1998 / Accepted: 13 October 1998     

Typical cyperoid reproductive structures in Lipocarpha humboldtiana and Ascolepis brasiliensis (Cypereae – Cyperoideae – Cyperaceae): New evidence from a development perspective

Ascolepis and Lipocarpha, Cyperaceae, have highly reduced reproductive structures and hypogynous scales that are controversially appreciated. Because of this, flowers and spikelets and, thus, inflorescences have been interpreted in different ways, which, in turn, has led to placing the two genera in different tribes. Some authors interpret spikelets in Ascolepis and Lipocarpha as many-flowered and the so-called hypogynous scales as homologous to the lateral scales of Hypolytrum, or consider these scales comparable to a Scirpus bristle. However, many other authors consider spikelets in Lipocarpha and Ascolepis to be a result of a reductional process from a many-flowered cyperoid spikelet to a single-flowered spikelet, where the adaxial and abaxial hypogynous scales may be seen as the respective prophyll and glume of the reduced spikelets. The latest molecular phylogenies of Cyperaceae show both genera nested in the Cyperus clade, forming, in turn, a clade together with the rest of the Cypereae genera having single-flowered spikelets and hypogynous scales. Alternatively, based on this, the scales of uncertain homology that accompany the Ascolepis and Lipocarpha flower might be seen as special reproductive formations, representing a synapomorphy of such clade, instead of relicts of an ancestor with many-flowered spikelets. In view of this, freshly collected inflorescences of Lipocarpha humboldtiana Nees and Ascolepis brasiliensis (Kunth) Benth. ex C. B. Clarke were studied using light and scanning electron microscopy, with the aim of elucidating the nature of the controversially interpreted reproductive structures of these species from a development perspective. Results show that the “hypogynous scales” simply represent vestigial structures derived from the reduction of typical cyperoid spikelets, rather than a perianth part or specialized formations emerging as evolutionary novelties. Two scales are typically generated in both species, one being abaxial and the other adaxial, homologous to a glume and a prophyll, respectively, which contrasts with the eprophyllate condition so far attributed to Ascolepis. In both cases, the inflorescence is a spike of reduced spikelets, and the floral development in L. humboldtiana and in A. brasiliensis follows the general ontogenetic pattern observed in Cyperoideae. These characteristics support the inclusion of both genera in the Cypereae tribe.     

Plant species microendemism and conservation of montane maquis in New Caledonia: two new species of Pancheria (Cunoniaceae) from the Roche Ouaïème

Two species of Pancheria (Cunoniaceae) described here, Pancheria minima J.C. Bradford and Pancheria ouaiemensis J.C. Bradford, draw attention to a recently recognized biodiversity pattern in New Caledonia. Montane maquis on acidic substrates, especially on the Roche Ouaïème, harbors numerous endemic species and is a rare and globally unique ecosystem. We cite 12 species, most described in the past several years, known only from the Roche Ouaïème in an area less than 10km². Overall, 27 species are known only from montane maquis and currently not found in a well-protected area. The major local threat to montane maquis habitat is anthropogenic fire, with climate change a possible long-term problem. Those montane maquis species known from one or two localities, occupying very small areas, and with declining habitat quality are critically endangered or endangered based on IUCN Red List criteria. Adding the Roche Ouaïème to the reserve system of New Caledonia is recommended to protect and manage a representative area of montane maquis on acidic substrates. A research strategy is proposed to identify species most at risk, locate possible unknown areas of montane maquis, and update taxonomic knowledge. A review of characters that vary among Pancheria species is provided, and the inflorescence architecture is described and diagramed. Both new Pancheria species occur at upper elevations in shrubby habitats. P. minima is remarkable in that the size of plants, leaves and reproductive parts is highly reduced compared to other known species.