Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola

Xanthomonas oryzae pv. oryzicola is an important bacterial pathogen responsible for outbreaks of bacterial leaf streak (BLS) on rice, mostly occurring in Asia and parts of Africa. To better monitor epidemics and assess population structures, efficient tools that allow the precise identification and diagnosis of pathogenic populations are needed. In this study, we explored variable numbers of tandem repeats (VNTR) as a fast, reliable, and cost-effective molecular typing tool. Screening of three X. oryzae pv. oryzicola genome sequences (Philippine strain BLS256, Chinese strain GX01, and Malian strain MAI10) predicted 28 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 28 loci were designed and applied to a panel of 20 X. oryzae pv. oryzicola strains originating from Asia and Africa. Sequencing of PCR amplicons revealed 25 robust and polymorphic VNTR loci that are shared among Asian and African X. oryzae pv. oryzicola strains. A dendrogram constructed from 25 VNTR loci indicated that most Asian strains are clearly discriminated from African strains. However, in agreement with previous reports, one strain from Mali is related to Asian strains, pointing to a possible introduction of Asian strains to the African continent. The new VNTR-based tool described here is useful for studies of population structures and epidemiological monitoring of X. oryzae pv. oryzicola.     

The multilayer model of soil mineral–organic interfaces—a review

Association of organic matter (OM) with minerals is an important pathway in the formation of stable OM in soil. While the importance of mineral–organic associations (MOA) in regulating soil carbon cycling has been rigorously demonstrated by empirical evidence, knowledge about the molecular‐scale arrangement of OM at mineral surfaces is still lacking. Such knowledge is urgently needed to disentangle the mechanisms of long‐term storage of soil OM. Based on indirect observations regarding the formation, composition, and structure of MOA, a conceptual multilayer model was proposed by Kleber et al. in 2007 to foster debate and help elucidating the structure and reactivity of MOA. According to this model, the associated OM at mineral surfaces is discrete and self‐organized into a multilayer structure. In this review, we aim to collect and evaluate existing studies that used this model to explain biogeochemical processes at mineral–organic interfaces, and based on this, assess the applicability of the model. The multilayer model has seen extensive adoption within soil science and related fields. In general, existing studies either support the concept of a patchy distribution of adsorbed OM on mineral surfaces or advocate that OM can be coprecipitated with nanosized poorly crystalline minerals or hydrolysable metals. However, the evidence for the patchy distribution of adsorbed OM cannot support the multilayer model on its own. There is little consensus about the role of N‐rich OM in forming the contact zone according to the multilayer model but surface conditioning by different classes of organic compounds appears to be an essential factor for the overall adsorption of OM. Nevertheless, large uncertainty still remains with respect to multilayer‐like organization of MOA. By taking advantage of recent developments in surface analytical sciences and computational chemistry, a rigid experimental testing of the multilayer model at the molecular level is still required and awaits to be integrated into improved concepts of MOA formation and OM stabilization.     

Sediment imbalances and flooding risk in European deltas and estuaries

Purpose

We analysed the status of current water and sediment management practices in six deltas and estuaries, which were part of the European DELTANET, INTERREG-funded network.

Materials and methods

These systems—the Danube, Ebro and Vistula deltas and the Elbe, Minho and Severn estuaries—represent different geographic regions of Europe. This enables comparison between the sites’ approaches to common coastal issues, notably those associated with sediment budgets, contamination and flood risk. Based on documentary analysis, workshop events and expert discussion, we employ a simple classification scheme to distinguish between levels of risk from these aspects.

Results

We suggest that flood risk is the most significant risk, followed by upstream sediment retention and sediment aggradation. Chemical contamination, though less severe, is not unimportant. Key management issues include a lack of environmental quality standards for sediment and suspended particulate matter, as well as the limited deployment of monitoring programmes, regular sediment sampling and associated chemical analyses.

Conclusions

These include both general and specific recommendations. Within these, the limited scope of integrated plans that aim for sustainability of the respective systems is highlighted. It is suggested that these do not challenge traditional, classical engineering approaches sufficiently. Nor do they address the origin of many environmental problems, especially those which are closely linked to short-term political and economic priorities.     

Chromosomal composition of the genome in the monomorphic diplokaryotic microsporidium Paranosema grylli: analysis by two-dimensional pulsed-field gel electrophoresis

The molecular karyotype of Paranosema grylli Sokolova, Seleznev, Dolgikh et Issi, 1994, a monomorphic diplokaryotic microsporidium, comprises numerous bright and faint bands of nonstoichiometric staining intensity. Restriction analysis of chromosomal DNAs by "karyotype and restriction display" 2-D PFGE has demonstrated that the complexity of molecular karyotype of P. grylli is related to the pronounced length polymorphism of-homologous chromosomes. The background of this phenomenon is discussed in the context of ploidy state, reproductive strategy and population structure in this microsporidium. We propose that the remarkable size variation between homologous chromosomes in P. grylli may be a consequence of ectopic recombination at the chromosome extremities.     

The Genus <Emphasis Type="Italic">Fragaria </Emphasis>in Croatia

Only three native species of genus Fragaria (F. moschata, F. vesca and F. viridis) are recorded in three regions of Croatia. These species as well as many of their hybrids, are, or once were, cultivated for their edible fruits. The majority of cultivated strawberries in Europe belong to garden strawberries F. x ananassa (hybrids of F. chiloensis and F. virginiana). The most expanded wild strawberry species in Croatia is a woodland strawberry (F. vesca) whose berries are gathered seasonally as wild edible fruits. They often contain higher amount of nutrients and bioactive compounds in comparison to cultivated varieties. The research on the genus Fragaria species distribution in Croatia has not been carried out, and so is the case with many others wild growing fruit species in Croatia. By summing up a number of individual citations and observations, it is possible to get a perspective regarding the current state of their distribution.     

Response of Potato (Solanum tuberosum L.) Germplasm to Water Stress Under In Vitro Conditions

Chile is center of origin and diversity of potato (Solanum tuberosum L.). Potato yield is affected under water stress conditions, so development of varieties with better tolerance to this stress is desirable. In this study we determined the differential response of INIA-Chile potato germplasm to water stress under in vitro assays with polyethylene glycol. One-hundred-and-fourty-nine genotypes were evaluated. Polyethylene glycol 4.8 % w/v was able to distinguish genotype response by considering the morphological variables (plantlet height, leaf and root number) and fresh and dry weight. Through multivariate statistical analysis, and in comparison with their respective controls without treatment, genotypes were clustered with high (74 – 79 %), intermediate (29 – 94 %), low (29 – 57 %), and very low (4– 28 %) water stress tolerance. The high-tolerance-response cluster was mainly made up of Chilean potato landraces. These results highlight the importance of this germplasm in food security, which could be directly cultivated and/or be used as progenitors to produce new varieties with increased tolerance to water-deficit stress.     

Dynamic models applied to giant barnacle culture

In this study, a dynamic model is applied to giant barnacle (Austromegabalanus psittacus) spat collection from artificial substrates located in the wild. Semi-industrial culture of the giant barnacle, A. psittacus “picoroco” in southern Chile is an interesting option for aquaculture diversification. The model establishes relationships between variables and carries out simulations to determine their effects on spat provision. The dynamic hypothesis proposes that the number of giant barnacle spat obtained from the wild is influenced by competent larval abundance (cyprids) over time, substrate availability and mortality after larval settlement. In the conceptual model, 15 variables were selected and related, establishing the polarities of each causal relationship and of each feedback loop. The Stock & Flow diagram was undertaken using STELLA 9.0 simulation software. Simulation tests were carried out to establish the consistency of the model using the empirical background obtained from semi-industrial cultures in southern Chile. The model establishes relative quantity of competent larvae, substrate area and the number of spat, as key variables. Synchrony between level of cyprid abundance and location of artificial substrates in the water is critical to achieve maximum collector efficiency. A difference of less than 1 week out of synchronization produces significant losses (60–70%) in spat production. When the deployment of collectors and maximum quantity of competent larvae are synchronized, sensitivity analysis establishes an increase of up to 49.4% in the number of spat, as a result of the collector area released by spat early mortality. The application of dynamic models in aquaculture constitutes a useful tool for optimizing the process. The model proposed enables us to understand the processes associated with obtaining seed from the environment and can be applied to other similar processes, such as mytilid cultures.     

Marine Derived Hamacanthins as Lead for the Development of Novel PDGFRβ Protein Kinase Inhibitors

In this study, we report on pyrazin-2(1H)-ones as lead for the development of potent adenosine triphosphate (ATP) competitive protein kinase inhibitors with implications as anti-cancer drugs. Initially, we identified the pyrazin-2(1H)-one scaffold from hamacanthins (deep sea marine sponge alkaloids) by Molecular Modeling studies as core binding motif in the ATP pocket of receptor tyrosine kinases (RTK), which are validated drug targets for the treatment of various neoplastic diseases. Structure-based design studies on a human RTK member PDGFR (platelet-derived growth factor receptor) suggested a straight forward lead optimization strategy. Accordingly, we focused on a Medicinal Chemistry project to develop pyrazin-2(1H)-ones as optimized PDGFR binders. In order to reveal Structure-Activity-Relationships (SAR), we established a flexible synthetic route via microwave mediated ring closure to asymmetric 3,5-substituted pyrazin-2(1H)-ones and produced a set of novel compounds. Herein, we identified highly potent PDGFR binders with IC₅₀ values in an enzymatic assay below µM range, and possessing significant activity against PDGFR dependent cancer cells. Thus, marine hamacanthin-derived pyrazin-2(1H)-ones showing interesting properties as lead for their further development towards potent PDGFR-inhibitors.