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.     

Food resources and cyprinid diet in permanent and temporary Mediterranean rivers with natural and regulated flow

This study addresses the differences in food availability, diet and feeding activity of the Iberian barbel, between permanent and temporary nonregulated rivers, and the effect of flow regulation on feeding parameters. A total of 267 adult barbels were seasonally collected in four nonregulated and regulated rivers from permanent and temporary basins, and their gut content was analysed. Locally available food sources were evaluated across sites and seasons. Barbels from the permanent nonregulated river exhibit a more variable and diversified diet in which invertebrates assumed a large importance, especially during high flows. Barbels from the temporary nonregulated river presented a more uniform diet composed of plant material and detritus, particularly in drought seasons. Flow regulation affected different flow components in both systems, but the effects on food resources and barbels' diet were similar, resulting in an intra‐annual stabilisation of resource availability and fish diet, with a higher consumption of plants and detritus. Changes in fish diet and feeding activity in both nonregulated and regulated rivers were strongly associated with the seasonal variability of streamflow components, particularly between low‐ and high‐flow periods, and with the reduction in flow variability in the case of dam regulation. Results from this study can be used to improve guidelines for flow requirement implementation.     

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.     

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.     

Detection of Leishmania spp. and associated inflammation in ocular‐associated smooth and striated muscles in dogs with patent leishmaniosis

Objective Canine leishmaniosis is a disease characterized by the wide distribution of the parasite throughout the tissues of the host. The purpose of this study was to describe the presence of Leishmania spp. and associated inflammation in ocular‐associated muscles of dogs with patent leishmaniosis. Procedures Smooth muscles (iris dilator muscle, iris sphincter muscle, ciliary muscle, Müller muscle, smooth muscle of the periorbita and smooth muscle of the nictitating membrane) and striated muscles (orbicularis oculi muscle, obliquus dorsalis muscle and dorsal rectus muscle) were evaluated. Routine staining with hematoxylin and eosin and immunohistochemistry to detect Leishmania spp. were performed on tissue sections. Results Granulomatous inflammation was seen surrounding muscular fibers and was composed mainly of macrophages with scattered lymphocytes and plasma cells. This infiltrate could be seen in 52/473 (10.99%) samples of smooth muscle and 36/142 (25.35%) samples of striated muscle. Parasites were detected in 43/473 (9.09%) samples of smooth muscle and in 28/142 (19.71%) samples of striated muscle. Conclusions To the authors’ knowledge, this is the first report assessing the presence of Leishmania spp. and associated infiltrate in intraocular, extraocular and adnexal smooth and striated muscles. The inflammation present in those muscles could contribute to clinical signs already described, such as blepharitis, uveitis, and orbital cellulitis.     

Chemopreventive activity of polyphenolics from black Jamapa bean (Phaseolus vulgaris L.) on HeLa and HaCaT cells

The antiproliferative effects of 100% methanol crude extract and of Toyopearl and silica gel fractions from the seed coats of black Jamapa beans (Phaseolus vulgaris L.) were evaluated using HeLa, human adenocarcinoma cells, and HaCaT, human premalignant keratinocytes. The 100% methanol crude extract [172.2 microM equiv of (+)-catechin] increased adhesion of HeLa cells; however, 3- and 5-fold higher concentrations decreased the number of cells attached as a function of the treatment time. The highest concentration tested diminished the cell adhesion until 40% (after 24 h) to almost 80% (after 72 h). The IC50 values showed that the 100% methanol crude extract was the most effective inhibitor of HeLa cell proliferation, even when it was dissolved in dimethylsulfoxide (DMSO) [34.5 microM equiv of (+)-catechin] or in medium [97.7 microM equiv of (+)-catechin]. The Toyopearl 5 (TP5) fraction and silica gel 2 (SG2) fraction inhibited 60% of the HeLa cell proliferation. The IC50 was 154 microM equiv of (+)-catechin of the 100% methanol crude extract on HaCaT cells. Toyopearl fractions TP4 and TP6 significantly inhibited HaCaT cell proliferation, but the silica gel fractions did not have a significant effect. The 100% methanol crude extract (35 microg of dry material/mL) decreased the number of HeLa cells in the G0/G1 phase from 68.9% (for control cells) to 51.4% (for treated cells) and increased apoptosis (2.9 and 21.2% for control and treated cells, respectively). The results indicated that black Jamapa beans could be a source of polyphenolic compounds, which have an inhibitory effect toward HeLa cancer cells but are less aggressive on HaCaT premalignant cells.     

Cardiomyocyte calcium cycling in a naturally occurring German shepherd dog model of inherited ventricular arrhythmia and sudden cardiac death

ObjectiveTo further characterize arrhythmic mechanisms in German shepherd dogs (GSDs) affected with inherited ventricular arrhythmias by evaluating intracellular calcium cycling and expression of calcium handling genes.AnimalsTwenty five GSDs, 9 backcross dogs, and 6 normal mongrel dogs (controls) were studied. The GSDs and backcross dogs were from a research colony of inherited ventricular arrhythmias. The control research dogs were purchased.MethodsAction potentials (APs) and pseudo-electrocardiograms (ECG) were recorded from left ventricular (LV) wedge preparations of GSDs and normal dogs. Midmyocardial (Mid) LV cells from GSDs and normal mongrels were isolated by enzymatic digestion. Cells were either field stimulated or voltage clamped and calcium transients were measured by confocal microscopy using the indicator Fluo-3AM. Expression of calcium handling genes was measured by quantitative RT-PCR.ResultsMean calcium transient decay (tau) was not different between affected GSDs and control dogs, but striking cell-to-cell variability for tau was observed within affected GSDs and between affected GSDs and controls (P < 0.0001 each); within-dog variability accounted for 75% of total variability. Calcium sparks and afterdepolarizations occurred in GSD but not control cells. ATP2A2/SERCA2a expression was significantly reduced (P = 0.0063) in affected GSDs and inversely correlated (P = 0.0006) with severity of ventricular arrhythmias.ConclusionsGerman shepherd dogs with inherited ventricular arrhythmias have electrophysiologic abnormalities in calcium cycling associated with reduced ATP2A2/SERCA2a expression. These animals provide a unique opportunity to study calcium remodeling at the genetic and molecular level in familial ventricular arrhythmias.     

Bridging the Gap between Centrally Defined Policies and Local Decisions – Towards more Sensitive and Creative Rural Landscape Management

European policies and instruments such as the Common Agricultural Policy (CAP) and many instruments for nature and landscape conservation in Europe have for some decades been dominated by centralisation and standardisation. This paper shows that this has led to the neglect of contextual and place-related approaches and an unnecessarily high degree of over-simplification. Recently, as a reaction to this over-simplification, diversity and specific character has been particularly stressed in many European and national strategies for rural landscapes and conservation, but the processes of simplification still continue. Using examples from mixed agriculture and forestry landscapes in Portugal, Slovenia and Sweden, this paper aims to contribute to understanding the gap between centrally defined strategies for rural landscapes and awareness and management practices at local level. The three countries are situated at the outer fringes of Europe, and are complementary with their different degrees of urbanisation, forest distribution and tree-richness in the agricultural landscapes. Furthermore, the aim is to show how local landscape management is driven and to identify factors contributing to a better use of public policies through a participatory process with visions for the future. Systems of landscape classifications such as landscape character assessment often recognise the specific character of these landscapes, but have so far achieved very little for the preservation of their locally specific values, nor have they contributed to the development and the creation of new visions for future management. Such systems could contribute much more if they could be opened to adaptation on a more local scale in communication-led management planning.