A new protocol for assessing the conservation priority of groundwater‐dependent ecosystems

1. Species of conservation concern are usually considered important elements in site prioritization for biodiversity conservation. To overcome the lack of information on species conservation status, multidimensional measures of species rarity can be used as proxies of species vulnerability.
2. Under this assumption, a two‐step protocol for site prioritization of aquatic groundwater‐dependent ecosystems is proposed using invertebrate vulnerability estimated from species' traits. In the first step, each species occurring in the sites of interest are scored according to their vulnerability. In the second step, sites are prioritized using species' scores.
3. Species vulnerability scores are based on five dimensions, for which various traits are scored: (i) geography, (ii) ecology, (iii) biology, (iv) population, and (v) evolutionary history. For each species, the scores of the various traits belonging to the same dimension are multiplied to obtain a synthetic score. These scores are then ranked into four classes and, for each dimension, each species receives a new score that reflects its rank. The sum of these scores represents the species' overall score.
4. Site conservation priorities are assessed by combining species scores into three indices: Sum of Species Scores, Biodiversity Conservation Concern (which relates the sum of species scores with the local species richness) and Groundwater Biodiversity Concern (which is the average of the former two). The protocol is illustrated using case studies in Italy and it is fully implemented in the software AQUALIFE which is freely available at: http://app.aqualifeproject.eu by registered users.
5. Sensitivity analyses showed that the protocol is robust against the lack of information on species biology or sampling limitations. However, trait scoring rests with the user, who must be familiar with the study group.
6. This approach can be applied at any spatial scale and to different types of aquatic groundwater‐dependent ecosystems.

     

Genetic characterization of influenza A viruses circulating in pigs and isolated in north-east Spain during the period 2006–2007

Swine influenza virus is one of the most important pathogens involved in the swine respiratory disease complex. Recent serological surveys showed a high prevalence of swine influenza strains belonging to the H₁N₁, H₁N₂ and H₃N₂ subtypes circulating in pigs in Spain. However, little is known about their genome sequence. Five swine influenza strains were isolated from some unrelated outbreaks occurred during 2006–2007, and their complete genome sequences were determined. Phylogenetic analysis revealed that they belonged to the lineages “Avian-Like” H₁N₁, “Human-Like” H₃N₂, and “Human-Like” H₁N₂, showing tight relationships with early or contemporary strains described in Europe. Notably, one virus of the H₁N₂ subtype showed genetic and antigenic divergence with the European contemporary strains or vaccinal strains of the same subtype, suggesting that some local and divergent clusters of the virus may pass unnoticed in routinary subtyping. Finally, analysis on the entire pattern of genome segments suggested that a second reassortment event could have influenced the evolution of that divergent H₁N₂ strain.     

Extraction,semi-quantification,and fast on-line identification of oligopeptides in Grana Padano cheese by HPLC-MS

Sixteen samples of Grana Padano cheese aged from 2 to 33 months were analyzed by HPLC-MS. The extraction process involved the use of diluted HCl, thus avoiding a strong deproteinizing agent (TCA), and allowing to maintain in solution also very lipophilic peptides. The molecular mass of the most abundant peptides were determined by electrospray ionization (ESI) mass spectrometry. A new method was developed based on the small fragmentation peaks arising from in-source fragmentation and from software analysis of the known casein sequences, which in many cases allowed the direct on-line identification of the oligopeptide sequences. Several new peptides never previously reported were identified, some of which containing bioactive sequences, consistently with what was described in the literature. Semiquantification of peptides at the different stages of aging was also performed by using a suitable internal standard, providing new insights into the evolution of the oligopeptide fraction during aging.     

Active oxygen detoxifying enzymes and phenylalanine ammonia-lyase in the ethylene-induced chilling tolerance in citrus fruit

The effects of applying ethylene (2 microL x L(-)(1)) during cold storage of Fortune mandarins on the development of chilling-induced peel damage and on changes in the activities of the enzymes of the antioxidant system, superoxide dismutase, catalase (CAT), ascorbate peroxidase, guaiacol peroxidase, and glutathione reductase, and on phenylalanine ammonia-lyase (PAL) have been investigated. Chilling damage was reduced by applying ethylene during fruit storage at 1.5 degrees C. PAL activity increased in response to cold stress and was higher in fruit held under ethylene than under air during the whole storage period, whereas CAT was temporarily higher in ethylene-treated fruit. In contrast, the activities of the other enzymes were not increased by ethylene. The global results suggest that the ethylene-induced chilling tolerance in Fortune mandarins might be due to increased PAL and CAT activities.     

Genome‐wide analysis of homozygosity regions in european simmental bulls

The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH‐based coefficient of inbreeding (F_ROH) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) F_ROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome‐wide ROH‐traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.     

Quantification of Bacterial Populations Indigenous to Acidic Drainage Streams

Acid mine drainage (AMD) from mining activities can cause majorenvironmental problems. The acidity is due in part to the microbial oxidation of sulfide minerals in the exposed ores. Aslittle is known about seasonal variations of microbial populationsizes in AMD, the objective of this investigation was to quantifythe principal bacterial populations (iron-oxidizing acidophiles, sulfur-oxidizing acidophiles, sulfur-oxidizing neutrophiles, andacidophilic heterotrophs), with respect to season. The AMD sites sampled were four streams emerging from a copper/nickel tailingsarea. All bacterial populations with the exception of acidophilicsulfur oxidizers were recovered throughout the year. The most numerous bacteria were acidophilic heterotrophs and iron-oxidizing acidophiles. Surprisingly, there were no obvious trendsin the relative abundance of the various bacterial groups as a function of season. Recovery of the various bacterial groups at an incubation temperature of 4 °C indicated that psychrotrophic members do exist. During the course of the investigation, it was observed that thenumber of Acidithiobacillus ferrooxidans (Thiobacillusferrooxidans) colonies recovered on iron salts purified agarose,a preferred medium, was highly variable. The variability was attributed to the presence of non-iron-oxidizing satellite bacteria, the growth of which could be suppressed by increasingthe concentration of the electron donor ferrous sulfate.     

Maize grain production,plant nutrient concentration and soil chemical properties in response to different residue levels from two previous crops

ABSTRACT

The incorporation of previous crop residues in agricultural management benefits soil fertility, crop production, and environment. However, there is no enough information about maximum residue application level without negative effect over next crop yield. To evaluate maize (Zea mays L.) yield under short-time conservation management with incorporation and/or importation of different residue levels, a biannual rotation experiment was conducted in ash volcanic soil in south-central Chile. The experiment consisted of two previous crops, canola (Brassica napus L.) and bean (Phaseolus vulgaris L.), and four levels of residue incorporation (0%, 50%, 100%, and 200% of generated residue; from 0 to 21.4?Mg?ha^?1 for canola and from 0 to 19.0?Mg?ha^?1 for bean). Previous crop species and residue level affected some nutrients concentrations in grain and plant and some soil chemical properties, without effect in maize yield, which averaged 16.6?Mg?ha^?1. Bean residue increased Ca and reduced S in maize plant, increasing soil P, Ca, Mg and K (P?<?0.05). Maize grain Ca content was positively and proportionally affected by canola residue level and negatively and proportionally affected by bean residue level. All canola residue levels increased soil pH and Mg, but the highest level reduced soil S; soil P concentration increased proportionally with bean residue level. The highest bean residue level increased soil S. Different crop and levels of residue did not affect maize yield but did some plant nutrient concentration, and also affected some soil chemical properties.