Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus)

Many estimators and algorithms have been developed to infer the genealogical relationships from molecular marker data when there is no pedigree information. Most pairwise methods provide estimates in a continuous range that needs to be converted into genealogical relationships (namely full-sibs, half-sibs and unrelated) if there is a previous knowledge of the population structure. Transformations are usually based on arbitrary thresholds, but the possibility of correcting the coancestry estimates via explicit pedigree reconstruction methods has been suggested. Using molecular data for ten highly polymorphic microsatellite loci on a population of turbot (Scophthalmus maximus) with a known genealogy, the behaviour of four pairwise marker-based coancestry estimators and the molecular coancestry has been evaluated. The population consisted on 138 families with 4 full-sib individuals each and one family with 8 full-sib individuals (up to 15 half-sib families were also present due to the sharing of parents between some of the full-sibs families). Our results suggested that transforming the pairwise estimators and the molecular coancestry to family relationships through the establishment of thresholds performs slightly better than the explicit pedigree reconstruction method, when accuracy is measured in a pairwise basis. However, if joint relationships between more than two individuals were tested at a time, the threshold methods led to a high percentage of incongruous triads of full-sib individuals, with Mendelian incompatibilities appearing in congruous full-sib families (more than 70% and 60% in our study, respectively). The explicit pedigree reconstruction approach, due to its nature, is free from such problems. Therefore, the pedigree reconstruction approach seems to be a valuable tool to provide a congruent and compatible pedigree when the pairwise marker-based coancestry matrices or the molecular coancestry need to be transformed.     

Airborne fungal succession in a rice field of Cuba

This study characterised the airborne mycobiota of a rice plantation in Bauta (Havana, Cuba), with a view to improving crop quality. Culturable airborne fungi were sampled between March 2007 and February 2008 using a volumetric method (SAS Super 100) with potato dextrose agar as culture medium. The total fungal count was 51,425 cfu/m³. The 39 filamentous genera identified included several major rice pathogens (Bipolaris, Curvularia, Alternaria, Pyricularia, Cercospora and Fusarium) as well as potentially mycotoxigenic species of Fusarium, Penicillium and Aspergillus. Analysis of the influence of weather-related factors on spore counts revealed that total counts and Penicillium counts correlated positively with daily relative humidity, mean temperature and dew point.     

Comparative Characterization of Enzymatic Digestion from Fish and Soybean Meal from Simulated Digestive Process of Pacific Bluefin Tuna,Thunnus orientalis

The digestive process of the Pacific bluefin tuna (PBT), Thunnus orientalis, was simulated through two phases of in vitro digestion: acidic digestion with porcine pepsin, followed by alkaline digestion with pancreatic crude extract (PCE) obtained from the PBT to hydrolyze fish meal (FM) and soybean meal (SBM) as protein substrates. The crude protein from FM resulted in a lower degree of hydrolysis (73.3%) compared with SBM (79.2%). However, the resulting digested products showed that FM contained 35% more small peptides, with sizes <6.5 kDa than those from the starting material (>150 kDa). The SBM had an increase of only 1.3% in the similar peptide cut‐offs found after hydrolysis. These results suggested that FM appeared to be a better source of protein according to the amount of low‐molecular weight peptides. In addition, the proteolytic activity of PCE showed that 88.9% of its alkaline proteolytic activity corresponded to trypsin and 2.9% corresponded to chymotrypsin activity. The results shown here demonstrate that peptide sizes are important in identifying suitable protein sources for aquafeed production to reinforce the primary results obtained from the in vitro digestibility using the pH‐Stat system. These results also contribute to a better understanding of the digestibility process in aquatic organisms.     

Effect of tylosin on dogs with suspected tylosin-responsive diarrhea: a placebo-controlled,randomized, double-blinded,prospective clinical trial

Background

The macrolid antibiotic tylosin has been widely used to treat canine chronic diarrhea, although its efficacy is based on anecdotal reports and experimental studies in dogs and not on strong scientific evidence. The term tylosin-responsive diarrhea (TRD) refers to diarrheal disorders responding to tylosin therapy within a few days. In TRD, the stool remains normal as long as tylosin treatment continues, but diarrhea reappears in many dogs within weeks after discontinuation. The aim of our trial was to assess the effect of tylosin on fecal consistency compared with a placebo treatment in dogs with suspected TRD and additionally to establish whether tylosin in dogs with recurrent diarrhea is as effective as empirical studies and anecdotal reports suggest.

Methods

Subjects comprised 71 client-owned dogs that, according to the owners, had previously been treated successfully with tylosin due to recurrent diarrhea of unknown etiology. At the initial examination, where there were no signs of diarrhea, the dogs were randomly assigned in a 2:1 ratio to a tylosin or placebo group. During a two-month follow-up the owners evaluated the fecal consistency according to previously published guidelines. When diarrhea recurred, either tylosin (25 mg/kg q 24 h, 7 days) or placebo treatment was initiated orally. Treatment outcome was evaluated as the mean of fecal consistency scores assigned during the last three days of the treatment period. To test for differences between the tylosin and placebo group in the proportion of responders, Pearson''s Chi-squared test and Fisher''s exact test were applied.

Results

Sixty-one dogs met the selection criteria and were followed for two months. During the follow-up 27 dogs developed diarrhea and either tylosin or placebo treatment was started. The proportion of dogs with normal fecal consistency at the end of treatment was 85% (17/20) in the tylosin group and 29% (2/7) in the placebo group (Pearson''s Chi-squared test p = 0.0049 and Fisher''s exact test two-sided, p = 0.0114).

Conclusions

Our findings indicate that tylosin is effective in treating recurrent diarrhea in dogs. The dose of 25 mg/kg once daily appears sufficient. No changes specific to TRD were detected in the examinations.     

The neuron-specific protein PGP 9.5 is a ubiquitin carboxyl-terminal hydrolase

A complementary DNA (cDNA) for ubiquitin carboxyl-terminal hydrolase isozyme L3 was cloned from human B cells. The cDNA encodes a protein of 230 amino acids with a molecular mass of 26.182 daltons. The human protein is very similar to the bovine homolog, with only three amino acids differing in over 100 residues compared. The amino acid sequence deduced from the cDNA was 54% identical to that of the neuron-specific protein PGP 9.5. Purification of bovine PGP 9.5 confirmed that it is also a ubiquitin carboxyl-terminal hydrolase. These results suggest that a family of such related proteins exists and that their expression is tissue-specific.     

Molecular Characterization of the USDA White Clover (Trifolium repens L.) Core Collection by RAPD Markers

White clover is one of the most important forage legume species worldwide, playing an important role in Southern Brazil temperate cultivated pastures. This work was aimed to characterize the genetic variability of the USDA white clover core collection formed by 78 accessions representing 50 countries, together with two very well known cultivars (Huia and Ladino Regal), using RAPD (Random Amplified Polymorphic DNA) markers to produce genetic fingerprints. There were used DNA bulks formed by the extraction and mixture of 20 random individuals from each accession. Twenty four primers were used, which revealed from 3 to 29 bands, forming a total of 371 polymorphic bans and only one monomorphic, ranging from 50 to 3098 bp. The results showed a genetic similarity among the accessions, ranging from 0.18 to 0.58 (Jaccard’s index), with an average of 0.24, allowing the identification of each individual accession using just three primers. The results also showed a large genetic variability within the white clover core collection, probably due to its reproduction mode and ploidy level, which could be used in plant breeding program.     

Rearing of pike-perch larvae using formulated diets – first success with starter feeds

The present study evaluated the performance of two commercial diets: AgloNorse (AN) and BioKyowa (BK), and two experimental, formulated diets based on casein (C) or casein plus casein hydrolysates (CH) in rearing of pike‐perch larvae (Sander lucioperca L.). All fish were 5 day old and control group was fed live Artemia nauplii. Fish were sampled periodically for histological comparison of morphological changes in the digestive tracts. Survival of fish fed Artemia nauplii, BK and AN was similar: 54.4%, 50.8% and 52.4%, respectively, while the fish fed formulated diets C and CH showed considerably lower survival: 28.4% and 21.6% respectively. After 5 weeks of rearing, the average body mass of fish ranged from 212±32 mg in Artemia fed group to 53.8±6.8 mg in C diet fed group. A considerable vacuolization of supranuclear zone in enterocytes of posterior intestine was observed in the larvae fed commercial diets. No anomalies in liver development were found. Hepatocytes of fish fed BK diet showed larger glycogen storage areas, compared with those occupied by lipids. The highest zymogen accumulation of pancreatic cytoplasm was observed in fish fed Artemia. In fish fed C and CH diets, anomalies in digestive system development were indicated by lower and less numerous intestinal folds, smaller hepatocytes, retarded development of gastric glands, and in CH group – also local fatty degeneration of liver.     

Microsatellite variability in natural populations of the blackspot seabream Pagellus bogaraveo (Brünnick, 1768): a database to access parentage assignment in aquaculture

Eight microsatellite loci previously reported were assessed for their utility in parentage assignment in 96 individuals belonging to natural populations of the blackspot seabream Pagellus bogaraveo (Brünnick, 1768) from the Mediterranean and Northeast Atlantic regions. At the mtDNA level, no differentiation was found between these two regions but based on microsatellite data an overall discrete genetic differentiation is perceivable between the two regions separated by the Strait of Gibraltar. The number of alleles per locus ranged from 8 to 30. A database constructed with allele frequency data from six populations was used in a simulation parentage assignment test using the software cervus . The test showed that the number of markers used is enough to perform parentage assignments with real data. The polymorphic information content for each locus was very high (mean value of 0.849), with a total exclusionary power of 0.9995. In summary, seven of the eight microsatellites analysed proved to be sufficient and powerful tools for parentage assignment in hatcheries and the allele frequency data given here can be used to perform pedigree analysis against which real data may be tested.     

Growth, stress response and free amino acid levels in Senegalese sole (Solea senegalensis Kaup 1858) chronically exposed to exogenous ammonia

Stressful husbandry conditions are likely to affect growth and amino acid metabolism in fish. In this study, chronic ammonia exposure was used to test the effects of a stressor on growth and amino acid metabolism of Senegalese sole juveniles. The fish were exposed for 52 days to 11.6 mg L⁻¹ [low‐TAN (L‐TAN)] or 23.2 mg L⁻¹ [high‐TAN (H‐TAN)] of total ammonia nitrogen (TAN), or to 0 mg L⁻¹ (Control). Growth in L‐TAN groups was slightly but significantly different from the Control groups [relative growth rate (RGR=0.35±0.13 and 0.52±0.23% day⁻¹ respectively)]. In H‐TAN groups, growth was severely affected (RGR=0.01±0.13% day⁻¹). Stress parameters (plasma cortisol and glucose) showed slight or no significant differences between treatments. Plasma free amino acid (FAA) concentrations were affected after H‐TAN treatment. Increases in glutamine and aspartate concentrations in H‐TAN fish suggest alterations in amino acid metabolism related to nitrogen excretion processes. Some of the changes in FAA concentrations also suggest mobilization to energy supply and synthesis of metabolites related to stress response. Therefore, Senegalese sole seem to adapt to the L‐TAN concentration tested, but the H‐TAN concentration reduced growth and affected amino acid metabolism.