Expert knowledge for translating land cover/use maps to General Habitat Categories (GHC)

Monitoring biodiversity at the level of habitats and landscape is becoming widespread in Europe and elsewhere as countries establish international and national habitat conservation policies and monitoring systems. Earth Observation (EO) data offers a potential solution to long-term biodiversity monitoring through direct mapping of habitats or by integrating Land Cover/Use (LC/LU) maps with contextual spatial information and in situ data. Therefore, it appears necessary to develop an automatic/semi-automatic translation framework of LC/LU classes to habitat classes, but also challenging due to discrepancies in domain definitions. In the context of the FP7 BIO_SOS (www.biosos.eu) project, the authors demonstrated the feasibility of the Food and Agricultural Organization Land Cover Classification System (LCCS) taxonomy to habitat class translation. They also developed a framework to automatically translate LCCS classes into the recently proposed General Habitat Categories classification system, able to provide an exhaustive typology of habitat types, ranging from natural ecosystems to urban areas around the globe. However discrepancies in terminology, plant height criteria and basic principles between the two mapping domains inducing a number of one-to-many and many-to-many relations were identified, revealing the need of additional ecological expert knowledge to resolve the ambiguities. This paper illustrates how class phenology, class topological arrangement in the landscape, class spectral signature from multi-temporal Very High spatial Resolution (VHR) satellite imagery and plant height measurements can be used to resolve such ambiguities. Concerning plant height, this paper also compares the mapping results obtained by using accurate values extracted from LIght Detection And Ranging (LIDAR) data and by exploiting EO data texture features (i.e. entropy) as a proxy of plant height information, when LIDAR data are not available. An application for two Natura 2000 coastal sites in Southern Italy is discussed.     

Reconstructing the history of the sand tiger shark (Carcharias taurus) in the Mediterranean Sea

1. Sharks are globally exposed to several anthropogenic threats, which, in many cases, have severely reduced their distribution and have impacted populations. In the Mediterranean Sea, because of its long history of exploitation and the relatively short span of scientific monitoring, reconstructing shark baselines is challenging. Many vulnerable species declined in population abundance and geographic distribution before it was possible to adequately track these changes. Consequently, for many of these species, current conservation assessments are now suffering from a severe case of shifting baseline syndrome, whereby their historical occurrence in the area is questioned.
2. The sand tiger shark (Carcharias taurus) is one of these cases. Characterized by high philopatry, restricted home range, and low interchange between populations, its Mediterranean population may have been severely impacted by the high historical fishing pressure in the region before scientific monitoring began.
3. In this study, the history of the abundance and distribution of C. taurus in the Mediterranean Sea was reconstructed through a comprehensive search of occurrence records in the literature and in museum collections. Between 1810 and 2008, 31 occurrence records and 54 publications provided information on the presence of the species in the area. These records were sparse but systematic over time and indicated occurrence hot spots in the south‐western Mediterranean Sea and in the eastern Adriatic Sea.
4. The presence of ten sightings of juveniles from a total of 18 sightings with length information suggested local parturition. Habitat and extinction models indicate that the area has suitable oceanographic conditions for the occurrence of the species and that the species cannot be considered extinct in the Mediterranean Sea. Our study suggests that there is still hope for the recovery of the species and underlines the crucial role of historical investigations to reconstruct the history of large elasmobranchs in the Mediterranean Sea.

     

Historical DNA as a tool to genetically characterize the Mediterranean sand tiger shark (Carcharias taurus,Lamniformes: Odontaspididae): A species probably disappeared from this basin

1. The sand tiger shark (Carcharias taurus) is a coastal species distributed in temperate and sub‐tropical waters, classified as ‘Vulnerable’ at global level and ‘Critically endangered’ in eastern Australia, south‐western Atlantic Ocean, and Mediterranean Sea. Six populations (north‐western Atlantic, Brazil, South Africa, Japan, eastern Australia, and western Australia) with low genetic diversity and limited gene flow were identified worldwide, but genetic information for many other geographic areas are still missing. Specifically, this species is listed in several reports as part of the Mediterranean fauna, even if there has been a lack of catches and sightings in recent years in this basin. To clarify the origin of C. taurus individuals caught in the past in the Mediterranean Sea, historical samples were genetically analysed.
2. Nine samples with certain Mediterranean origin were collected from different European museums. DNA was extracted and ~600 bp of the mitochondrial DNA control region were amplified using eight overlapping species‐specific primer pairs. Sequences obtained were aligned with all the haplotypes globally known so far.
3. Genetic analysis revealed the misidentification of one museum specimen. Among the remaining Mediterranean historical samples, three different haplotypes were recovered. Two of them previously observed only in South Africa and one described in both South African and Brazilian populations.
4. Results suggest a genetic relationship between Mediterranean sand tiger sharks and those from the western Indian Ocean. According to previous studies, we hypothesized that, during the Pleistocene, the cold Benguela upwelling barrier was temporarily reduced allowing the passage of C. taurus individuals from the Indian to Atlantic Ocean. After the restoration of this phylogeographic barrier some individuals were trapped in the Atlantic Ocean and probably migrated northward colonizing the western African coasts and the Mediterranean Sea.

     

Distribution of Trace Elements in Soils from the Sudbury Smelting Area (Ontario,Canada)

The sequential extraction procedure proposed by the European Commission Measurement and Testing Programme, combined with Scanning Electron Microscopy and Energy Dispersive X-ray Analysis(SEM/EDS), was applied to identify and quantify the chemical andmineralogical forms of Cu, Ni, Fe, Mn, Zn, Pb, Cr and Cd presentin the topsoil from a mining and smelting area near Sudbury (Ontario, Canada). The possible mobility of the chemical forms was also assessed. The metal fractions: (1) soluble and exchangeable, (2) occluded in manganese oxides and in easily reducible iron oxides, (3) organically bound and in form of sulphides, (4) residual mainly present in the mineral lattice structures were separated. Cu and Ni were the major metallic contaminants, occurring in soils in broad ranges of concentrations: Cu 11–1890 and Ni 23–2150 mg kg^-1. Cu was uniformly distributed among allthe extracted fractions. Ni was found associated mainly withthe residual forms, accounting for 17–92%, with an averageof 64%, of the total Ni present in the soils. Fe, Mn, Zn,Pb, Cr and Cd, while occurring in most analysed samples innormal soil concentrations, were primarily held in theresidual mineral fraction (on average >50%). The solubleand exchangeable forms made a small contribution (≤8.1%)to the total content of metals extracted. At least 14% ofthe total Cd, Mn and Pb was mobilised from the reducibleforms. The oxidizable fraction assumed mean values higher than10% only for Pb and Zn. Statistical treatment of the experimental data showed significant correlations between totalmetal content of the soils, some soil properties such as pH value, clay and organic matter content, and metal concentrationsin the various fractions. SEM/EDS analysis showed Fe in form ofoxides and sulphides in soils and Cu, Ni, Mn, Zn and Cr in association with iron oxides. Numerous black carbonaceous particles and precipitates of aluminium fluoride salts, observedin the solid residue left after `total’ digestion, were found tocontain Fe, Ni and Cr.     

Correction of ADA-SCID by stem cell gene therapy combined with nonmyeloablative conditioning

Hematopoietic stem cell (HSC) gene therapy for adenosine deaminase (ADA)-deficient severe combined immunodeficiency (SCID) has shown limited clinical efficacy because of the small proportion of engrafted genetically corrected HSCs. We describe an improved protocol for gene transfer into HSCs associated with nonmyeloablative conditioning. This protocol was used in two patients for whom enzyme replacement therapy was not available, which allowed the effect of gene therapy alone to be evaluated. Sustained engraftment of engineered HSCs with differentiation into multiple lineages resulted in increased lymphocyte counts, improved immune functions (including antigen-specific responses), and lower toxic metabolites. Both patients are currently at home and clinically well, with normal growth and development. These results indicate the safety and efficacy of HSC gene therapy combined with nonmyeloablative conditioning for the treatment of SCID.     

Extractable iron and organic matter in the suspended insoluble material of fog droplets

In this work the formation and composition of aggregates between metals and organic material is studied in real fog samples. In a preliminary experiment it has been found that concentrated cloud samples form a yellow-brown precipitate in the presence of Fe(III). Standards of humic acids and fulvic acids co-precipitate with Fe(III), forming similar aggregates i.e. iron-humates (Fe-HA) and iron-fulvates (Fe-FA). By comparing the solubility properties of aggregates by extracting organic carbon (OC) in different pH conditions, it has been observed that fog droplet particulate samples are characterised by solubility properties more similar to those of Fe-HA than Fe-FA. Dilute alkaline solutions can also easily extract organic refractory substances that form aggregates with metals. The recoveries of the total extractable organic matter (accounting for 12% of total insoluble carbon and 15% of particulate mass) are similar to those of humic-like substances (HULIS) from particulate samples. The chromatographic behaviour and functional group characteristics measured in the alkali-extract fraction of precipitated aggregates with iron and in the insoluble particulate of fog samples, are those of humic-like material. Thus, soluble HULIS are able to interact with iron to form particulate, but the composition of a large fraction of insoluble organic carbon is still unknown. These findings have implications on the solubility and surface tension properties of fog droplets and can therefore potentially influence droplet formation, as well as cloud chemical and photochemical processes.     

Discospondylitis associated with three unreported bacteria in the dog

Three cases of discospondylitis in the dog, caused respectively by Pseudomonas aeruginosa, Enterococcus faecalis and Staphylococcus epidermidis, are reported. These bacteria have not previously been documented as being the cause of the condition in this species. The neurological involvement was severe in all three cases. Two dogs were paraplegic and one was tetraplegic, and one of the paraplegic dogs had no deep pain on the extremities of both pelvic limbs. All dogs were treated surgically with a satisfactory neurological recovery.     

Giardia duodenalis in colony stray cats from Italy

Giardia duodenalis is the most common intestinal protozoan in humans and animals worldwide, including eight morphologically identical assemblages, infecting pets, livestock, wildlife and human beings. Assemblages A and B are those with the higher zoonotic potential, and they have been detected in several mammals other than humans; the others (C to H) show a higher host specificity. Cats can harbour both the specific Assemblage F and the zoonotic ones A and B. Several studies have been carried out on G. duodenalis genotypes in cats; however, the role of this species in the epidemiology of giardiasis is still poorly understood. In this scenario, the present study carried out the detection and genetic characterization at sub-assemblage level of G. duodenalis from colony stray cats in central Italy. In the period 2018–2019, 133 cat faecal samples were analysed for the presence of G. duodenalis cysts by a direct immunofluorescence assay. Positive samples were subsequently subjected to molecular analyses for assemblage/sub-assemblage identification. Forty-seven samples (35.3%) were positive for G. duodenalis cysts by immunofluorescence. G. duodenalis DNA was amplified at SSU-rDNA locus from 39 isolates: 37 were positive for zoonotic Assemblage A and 2 showed a mixed infection (A + B). Positive results for the β-giardin gene were achieved for 25 isolates. Sequence analysis revealed 16 isolates belonging to Sub-assemblage AII and 8 to Sub-assemblage AIII. One isolate resulted as ambiguous AI/AIII. Large sequence variability at the sub-assemblage level was detected, with several double peaks and mutations, making complex a proper isolate allocation. When compared with previous studies, the 35.3% prevalence of G. duodenalis in cats reported in the present article was surprisingly high. Moreover, all positive cats resulted to be infected with zoonotic assemblages/sub-assemblages, thus indicating stray cats as a possible source of human giardiasis and highlighting the sanitary relevance of cat colonies in the study area.     

Cholecystocutaneous fistula containing multiple gallstones in a dog

A 7-year-old dog was presented with a history of an open lesion on the right thoracic wall, discharging honey-like fluid and small stones. Ultrasonography and computed tomographic fistulography identified a cholecystocutaneous fistula; cholecystectomy was curative. Veterinarians should consider this disease in patients with long-term discharging lesions on the right thoracic or abdominal wall.