Cold Adaptation of a Mesophilic Subtilisin-like Protease by Laboratory Evolution

Enzymes isolated from organisms native to cold environments generally exhibit higher catalytic efficiency at low temperatures and greater thermosensitivity than their mesophilic counterparts. In an effort to understand the evolutionary process and the molecular basis of cold adaptation, we have used directed evolution to convert a mesophilic subtilisin-like protease from Bacillus sphaericus, SSII, into its psychrophilic counterpart. A single round of random mutagenesis followed by recombination of improved variants yielded a mutant, P3C9, with a catalytic rate constant (kcat) at 10 °C 6.6 times and a catalytic efficiency (kcat/KM) 9.6 times that of wild type. Its half-life at 70 °C is 3.3 times less than wild type. Although there is a trend toward decreasing stability during the progression from mesophile to psychrophile, there is not a strict correlation between decreasing stability and increasing low temperature activity. A first generation mutant with a >2-fold increase in kcat is actually more stable than wild type. This suggests that the ultimate decrease in stability may be due to random drift rather than a physical incompatibility between low temperature activity and high temperature stability. SSII shares 77.4% identity with the naturally psychrophilic protease subtilisin S41. Although SSII and S41 differ at 85 positions, four amino acid substitutions were sufficient to generate an SSII whose low temperature activity is greater than that of S41. That none of the four are found in S41 indicates that there are multiple routes to cold adaptation

Semantic Enrichment of Ontology Mappings

Schema and ontology matching play an important part in the field of data integration and semantic web. Given two heterogeneous data sources, meta data matching usually constitutes the first step in the data integration workflow, which refers to the analysis and comparison of two input resources like schemas or ontologies. The result is a list of correspondences between the two schemas or ontologies, which is often called mapping or alignment. Many tools and research approaches have been proposed to automatically determine those correspondences. However, most match tools do not provide any information about the relation type that holds between matching concepts, for the simple but important reason that most common match strategies are too simple and heuristic to allow any sophisticated relation type determination. Knowing the specific type holding between two concepts, e.g., whether they are in an equality, subsumption (is-a) or part-of relation, is very important for advanced data integration tasks, such as ontology merging or ontology evolution. It is also very important for mappings in the biological or biomedical domain, where is-a and part-of relations may exceed the number of equality correspondences by far. Such more expressive mappings allow much better integration results and have scarcely been in the focus of research so far. In this doctoral thesis, the determination of the correspondence types in a given mapping is the focus of interest, which is referred to as semantic mapping enrichment. We introduce and present the mapping enrichment tool STROMA, which obtains a pre-calculated schema or ontology mapping and for each correspondence determines a semantic relation type. In contrast to previous approaches, we will strongly focus on linguistic laws and linguistic insights. By and large, linguistics is the key for precise matching and for the determination of relation types. We will introduce various strategies that make use of these linguistic laws and are able to calculate the semantic type between two matching concepts. The observations and insights gained from this research go far beyond the field of mapping enrichment and can be also applied to schema and ontology matching in general. Since generic strategies have certain limits and may not be able to determine the relation type between more complex concepts, like a laptop and a personal computer, background knowledge plays an important role in this research as well. For example, a thesaurus can help to recognize that these two concepts are in an is-a relation. We will show how background knowledge can be effectively used in this instance, how it is possible to draw conclusions even if a concept is not contained in it, how the relation types in complex paths can be resolved and how time complexity can be reduced by a so-called bidirectional search. The developed techniques go far beyond the background knowledge exploitation of previous approaches, and are now part of the semantic repository SemRep, a flexible and extendable system that combines different lexicographic resources. Further on, we will show how additional lexicographic resources can be developed automatically by parsing Wikipedia articles. The proposed Wikipedia relation extraction approach yields some millions of additional relations, which constitute significant additional knowledge for mapping enrichment. The extracted relations were also added to SemRep, which thus became a comprehensive background knowledge resource. To augment the quality of the repository, different techniques were used to discover and delete irrelevant semantic relations. We could show in several experiments that STROMA obtains very good results w.r.t. relation type detection. In a comparative evaluation, it was able to achieve considerably better results than related applications. This corroborates the overall usefulness and strengths of the implemented strategies, which were developed with particular emphasis on the principles and laws of linguistics

Integrated Serologic Surveillance of Population Immunity and Disease Transmission.

Antibodies are unique among biomarkers in their ability to identify persons with protective immunity to vaccine-preventable diseases and to measure past exposure to diverse pathogens. Most infectious disease surveillance maintains a single-disease focus, but broader testing of existing serologic surveys with multiplex antibody assays would create new opportunities for integrated surveillance. In this perspective, we highlight multiple areas for potential synergy where integrated surveillance could add more value to public health efforts than the current trend of independent disease monitoring through vertical programs. We describe innovations in laboratory and data science that should accelerate integration and identify remaining challenges with respect to specimen collection, testing, and analysis. Throughout, we illustrate how information generated through integrated surveillance platforms can create new opportunities to more quickly and precisely identify global health program gaps that range from undervaccination to emerging pathogens to multilayered health disparities that span diverse communicable diseases

A stochastic approach to rainfall-induced slope failure

Hazard

Conservation status of the St Paul's Island wall lizard (Podarcis filfolensis kieselbachi)

The population of the endemic Maltese wall lizard, Podarcis filfolensis, on the small island of Selmunett (10.9 ha), off the northeast coast of the island of Malta, has been described as a distinct subspecies P .f. kieselbachi. Selmunett is a protected site and its lizard is a protected species. Reports of a pronounced decline in the Selmunett lizard population were investigated by systematic visual estimates of lizard population density started in 1999. Since August 1999, population counts declined from a high of 18 individuals observed per hour to zero by August 2005. The rate of decline was greatest for juveniles and females. Numerous cases of predation of the lizards by rats were observed and such predation seemed to be the cause of the decline in lizard population; visual counts of daytime-active rats, also started in 1999, showed a large rat population on Selmunett. In turn, the rat population appeared to have increased as a result of organic waste left by human visitors to the islet. A rat eradication programme implemented in 2006–2007 exterminated rats from Selmunett by the summer of 2007, when a few lizards captured in 2004 and kept in captivity since were released back on the islet to augment what remained of the population there (some lizards were spotted by casual observers, even if none were recorded during the actual counts). It remains to be seen if this attempt at saving the Selmunett wall-lizard population has been successful.peer-reviewe

Occurrence of the alien Bedriaga's frog (Rana bedriagae) Camerano, 1882 in the Maltese Islands, and implications for conservation

We document the occurrence of Bedriaga’s frog Rana bedriagae Camerano, 1882 in the freshwater pool of L-Ghadira ta’ Sarraflu on the island of Gozo, one of the very few naturally occurring permanent bodies of water in the Maltese Islands, and a protected site. The frog is an alien species that appears to have been deliberately introduced in the late 1990s and to have established a breeding population at Ta’ Sarraflu and possibly at two other sites on Gozo and at one site on Malta. Spread of the alien seems to be through human agency, not natural dispersal. Occurrence of the alien frog may have an impact on the only native amphibian, the Painted frog Discoglossus pictus pictus Otth, 1837, a protected species, as well as on the biota of the freshwater systems where the alien occurs, which are within or in close proximity to, protected sites and candidate Natura 2000 Special Areas of Conservation.peer-reviewe