The Structural Difference of Isobaric N-Glycans of Two Microalgae Samples Reveals Taxonomic Distance

Microalgae of the Chlorella clade are extensively investigated as an environmentally friendly source of renewable biofuels and high-value nutrients. In addition, essentially unprocessed Chlorella serves as wholesome food additive. A recent study on 80 commercial Chlorella preparations revealed an unexpected variety of protein-linked N-glycan patterns with unprecedented structural features, such as the occurrence of arabinose. Two groups of products exhibited a characteristic major N-glycan isobaric to the Man2GlcNAc2XylFuc N-glycan known from pineapple stem bromelain, but tandem mass spectrometry (MS/MS) analysis pointed at two types of N-glycan different from the bromelain structure, as well as from each other. Here we report the exact structures of these two novel N-glycan structures, elucidated by nuclear magnetic resonance spectroscopy and MS/MS, as well as on their phylogenetic context. Despite their humble size, these two N-glycans exhibited a very different design with structural features unrelated to those recently described for other Chlorella-clade strains. The major glycans of this study presented several novel structural features such as substitution by arabinose or xylose of the internal N-acetylglucosamine, as well as methylated sugars. ITS1-5.8S-ITS2 rDNA barcode analyses revealed that the xylose-containing structure derived from a product primarily comprising Scenedesmus species, and the arabinose-containing glycan type related to Chlorella species (SAG211-34 and FACHB-31) and to Auxenochlorella. This is another example where characteristic N-glycan structures distinguish phylogenetically different groups of microalgae.

Evaluation of Rhophilin Associated Tail Protein (ROPN1L) in the Human Liver Fluke Opisthorchis viverrini for Diagnostic Approach

Tegumental and excretory-secretory proteins are reported as diagnostic antigens for human opisthorchiasis. Rhophilin associated tail protein1-like (OvROPN1L) protein of Opisthorchis viverrini sperm tail showed potential as a diagnostic antigen. The OvROPN1L recombinant fragments were assayed for diagnostic antigenicity for human opisthorchiasis using indirect ELISA. The strongest antigenic region was a N-terminus peptide of M1 - P56. One synthetic peptide (P1, L3-Q13) of this region showed the highest antigenicity to opisthorchiasis. Sera from other parasitic infections including Strongyloides stercoralis, hookworm, Taenia spp, minute intestinal flukes, Paragonimus spp showed lower reactivity to P1. Peptide P1 is located in the disordered N-terminus of ROPN1L supporting its suitability as linear epitope. In the Platyhelminthes the N-terminal sequence of ROPN1L is diverging with taxonomic distance further suggesting that peptide P1 has potential as diagnostic tool in the genus Opisthorchis/Clonorchis. It should be further evaluated in combination with peptides derived from other O. viverrini antigens to increase its diagnostic power.

The Capacity for Limb Regeneration During Metamorphosis is Broadly Conserved in the Coccinellidae

A standardized laboratory procedure tested the limb regeneration abilities of 18 populations (16 species) of lady beetles which were then scored, relative to unoperated controls, based on survival, the proportion regenerating the limb completely or partially, and the magnitude of developmental costs (delayed development, reduced body size) associated with limb ablation. Newly molted fourth instar larvae each had a single foreleg amputated at the base of the femur. All species except Propylea dissecta (Mulsant) showed some complete limb regeneration, with limb regeneration index (LRI) scores ranging from 0.025 to 0.905 out of a possible 1.00 (mean = 0.598). Eriopis connexa Germar, an aphidophagous neotropical species, scored the highest. Widely distributed species that dominate agricultural habitats all scored above 0.75, and the only herbivore, Henosepilachna argus (Geoffroy), scored second from lowest. Prolonged pupal development was the most common cost, occurring in nine species, and correlating negatively with regeneration. Taxonomic distance between species correlated with regeneration, but explained <5% of variation; principal component analysis indicated that the LRI was the main factor distinguishing species. We infer that this capacity is conserved, not because of any adaptive advantage conferred, but because the genes responsible are normally activated during pupal development to generate the adult body plan and reconstitute appendages with direct correspondence to larval progenitors. However, good regeneration capacity was associated with the ecological success of the species. In general, broad geographic distribution, guild dominance, polyphagy, interspecific competitiveness, phenotypic flexibility, and invasiveness were characteristics generally shared by species with high levels of regeneration.

Host Plants Influence the Symbiont Diversity of Eriosomatinae (Hemiptera: Aphididae)

Eriosomatinae is a particular aphid group with typically heteroecious holocyclic life cycle, exhibiting strong primary host plant specialization and inducing galls on primary host plants. Aphids are frequently associated with bacterial symbionts, which can play fundamental roles in the ecology and evolution of their host aphids. However, the bacterial communities in Eriosomatinae are poorly known. In the present study, using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we surveyed the bacterial flora of eriosomatines and explored the associations between symbiont diversity and aphid relatedness, aphid host plant and geographical distribution. The microbiota of Eriosomatinae is dominated by the heritable primary endosymbiont Buchnera and several facultative symbionts. The primary endosymbiont Buchnera is expectedly the most abundant symbiont across all species. Six facultative symbionts were identified. Regiella was the most commonly identified facultative symbiont, and multiple infections of facultative symbionts were detected in the majority of the samples. Ordination analyses and statistical tests show that the symbiont community of aphids feeding on plants from the family Ulmaceae were distinguishable from aphids feeding on other host plants. Species in Eriosomatinae feeding on different plants are likely to carry different symbiont compositions. The symbiont distributions seem to be not related to taxonomic distance and geographical distance. Our findings suggest that host plants can affect symbiont maintenance, and will improve our understanding of the interactions between aphids, their symbionts and ecological conditions.

Harmonisation of a large-scale historical database with the principles of the World Reference Base for Soil Resources

<p>The possibility of an adequate use of data and maps from historical soil surveys depends, to a large measure, on their harmonisation. Legacy data originating from a large-scale national mapping campaign, “Systematic soil survey of agricultural soils in Czechoslovakia (SSS, 1961–1971)”, were harmonised and converted according to the World Reference Base 2014 (WRB). Applying three different methods of taxonomic distance computation and quantitative analysis and reclassification of the selected soil properties, the conversion of so-called Basic soil representatives (BSR) – mapping soil units providing information about soil (type, subtype, variety) and lithology (parent material, texture, soil depth, skeleton content) – to their counterparts in the WRB has been effectuated. The results proved the good potential of the used methods for soil data harmonisation. The values of taxonomic distance correspond to the different concepts and settings of the soil classes in the harmonized soil classifications. Classes with specific and narrowly defined diagnostics, often with one or few strong and distinctive features, show close distances with their counterparts, and, often, have only one relevant counterpart. On the contrary, soils with variable soil properties were approximating several related units. The additional information on the soil skeleton content, texture, depth and parent material showed the potential in the specification of some units, though the harmonisation of the soil texture turned out to be problematic due to the different categorisation of soil particles. The resulting soil classes have been presented for each polygon (so-called soil district) as i) one to one conversion, when each BSR is converted to one, most probable, WRB soil class (Reference soil group, RSG) and ii) soil association corresponding to the three closest RSGs. The validation of the results in the study region showed an average overall accuracy for a one-to-one (59.4 %) conversion and a very good accuracy (83.8 %) for the polygons presented as soil associations. The conversion accuracy differed significantly in the individual soil units, and ranged from 92 % in Fluvizems to 0 % in Technosols and Histosols. The extreme cases of a complete mis-classification can be attributed to inconsistencies originating in the historical database and maps. The study showed the potential of modern quantitative methods in the legacy data harmonisation and also the necessity of a critical approach to historical databases and maps.</p><p>Supported by the Ministry of Agriculture of the Czech Republic, Project No. QK1820389.</p>

Harmonisation of a large-scale historical database with the actual Czech soil classification system

The possibility of the adequate use of data and maps from historical soil surveys depends, to a large measure, on their harmonisation. Legacy data originating from a large-scale national mapping campaign, “Systematic soil survey of agricultural soils in Czechoslovakia (SSS, 1961–1971)”, were harmonised and converted according to the actual system of soil classification and descriptions used in Czechia – the Czech taxonomic soil classification system (CTSCS). Applying the methods of taxonomic distance and quantitative analysis and reclassification of the selected soil properties, the conversion of two types of mapping soil units with different detailed soil information (General soil representative (GSR), and Basic soil representative (BSR)) to their counterparts in the CTSCS has been effectuated. The results proved the good potential of the used methods for the soil data harmonisation. The closeness of the concepts of the two classifications was shown when a number of soil classes had only one counterpart with a very low taxonomic distance. On the contrary, soils with variable soil properties were approximating several related units. The additional information on the soil skeleton content, texture, depth and parent material, available for the BSR units, showed the potential in the specification of some units, though the harmonisation of the soil texture turned out to problematic due to the different categorisation of soil particles. The validation of the results in the study region showed a good overall accuracy (75% for GSR, 76.1% for BSR) for both spatial soil units, when better performance has been observed in BSR. The conversion accuracy differed significantly in the individual soil units, and ranged from almost 100% in Fluvizems to 0% in Anthropozems. The extreme cases of a complete mis-classification can be attributed to inconsistencies originating in the historical database and maps. The study showed the potential of modern quantitative methods in the legacy data harmonisation and also the necessity of a critical approach to historical databases and maps.

Classification of Digital Mammograms Into Masses and Non-Masses using Texture Combination Features and SVM

This paper presents a framework for grouping of mammogram images into carcinogenic and non- carcinogenic images. In this paper, image is enhanced using nonlinear contrast enhancement algorithm and then segmented using internal and external mask segmentation. The features used in the proposed work are based on the texture feature which means that the segmentation results will have minimal impact on the classification results of mammograms into masses and non – masses. The features used are Contrast, Energy, Homogeneity, Entropy, Mean Intensity, Standard Deviation, Taxonomic distinctness, Taxonomic distance and learning takes place by Support Vector Machine. The algorithm was applied on Mammographic Image Analysis Society database and when compared with contemporary techniques , the results were improved.

The Economic Value of Biodiversity

Biodiversity is declining worldwide, and the costs of biodiversity losses are increasingly being recognized by economists. In this article, we first review the multiple meanings of biodiversity, moving from species richness and simple abundance-weighted species counts to more complex measures that take account of taxonomic distance and functionality. We then explain the ways in which protecting biodiversity generates economic benefits in terms of direct and indirect values. Empirical approaches to estimating direct and indirect values are presented, along with a selection of recent evidence on how substantial these values are. The use of asset accounting approaches to track biodiversity values over time is discussed, in the context of sustainable development paths. Finally, we review some important challenges in valuing biodiversity that remain to be solved.

Hierarchical Matching of Traffic Information Services Using Semantic Similarity

Service matching aims to find the information similar to a given query, which has numerous applications in web search. Although existing methods yield promising results, they are not applicable for transportation. In this paper, we propose a multilevel matching method based on semantic technology, towards efficiently searching the traffic information requested. Our approach is divided into two stages: service clustering, which prunes candidate services that are not promising, and functional matching. The similarity at function level between services is computed by grouping the connections between the services into inheritance and noninheritance relationships. We also developed a three-layer framework with a semantic similarity measure that requires less time and space cost than existing method since the scale of candidate services is significantly smaller than the whole transportation network. The OWL_TC4 based service set was used to verify the proposed approach. The accuracy of offline service clustering reached 93.80%, and it reduced the response time to 651 ms when the total number of candidate services was 1000. Moreover, given the different thresholds for the semantic similarity measure, the proposed mixed matching model did better in terms of recall and precision (i.e., up to 72.7% and 80%, respectively, for more than 1000 services) compared to the compared models based on information theory and taxonomic distance. These experimental results confirmed the effectiveness and validity of service matching for responding quickly and accurately to user queries.