Two-mode clustering of genotype by trait and genotype by environment data

In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and traits/environments. For two-mode clustering, we first scan all two-mode cluster solutions with all possible numbers of clusters using k-means. After deciding on the final numbers of clusters, we continue with a two-mode clustering algorithm based on a genetic algorithm. This ensures optimal solutions even for large data sets. We discuss the application of two-mode clustering to multiple trait data stemming from genomic research on tomatoes as well as an application to multi-environment data on barley.     

Resonance of scantlings indicates the stiffness even of small specimens of Eucalyptus from plantations

The aim of this study was to establish the relationship between the stiffness of scantlings, approaching structural size materials, and small specimens of 6-year-old Eucalyptus urophylla?×?grandis wood using a resonance technique. The correlation between the elastic modulus (E) of the scantlings in longitudinal vibration and small specimens in flexural vibration was r?=?75 when comparing the scantling values with the averaged values of the specimens per scantling. However, when the E of each single specimen was compared with its respective scantling, the coefficient of correlation decreased to r?=?0.64 in the longitudinal tests and r?=?0.61 in the flexural tests. A roughly linear correlation (r?=?0.59) between specific modulus and loss tangent was obtained for the small specimens of Eucalyptus. In short, the resonance technique rapidly provided a large, accurate data set of mechanical wood properties as required for high-throughput phenotyping in recent genetic studies.     

First report of Lagochilascaris (Nematoda: Ascarididae) eggs in a public park in Southern Brazil

Public parks, especially in developing countries, are places where stray animals run free and may contaminate the environment with different species of parasites. In an evaluation of environmental sanitation of these sites, soil samples were collected monthly from public parks in the Pelotas city, Rio Grande do Sul State, Southern Brazil. Eggs of the nematode Lagochilascaris sp. were found in a public playground. This is the first report of identification of this nematode in Southern Brazil.     

A longitudinal study of Neospora caninum infection on three dairy farms in Brazil

Neospora caninum is an apicomplexan protozoan parasite that is one of the most important infectious causes of abortion in both dairy and beef cattle in many countries. The objectives of this longitudinal study were to determine the prevalence, rates of vertical and horizontal transmission of N. caninum and hazard for culling of N. caninum-seropositive animals in three Brazilian dairy herds. Blood samples from all animals were collected nine times at each of the three farms over a two-year period. Serum was tested for antibodies against N. caninum using the indirect fluorescent antibody test with a cutoff value of 1:100. The percentage of N. caninum-positive samples at each sampling time ranged at Farm I from 3.32% to 11.71%, at Farm II from 3.90% to 22.06% and at Farm III from 3.90% to 22.06%. The number of positive serological reactions varied in relation to the number of repeated samples taken from individual animals at each farm. In all herds, there was a high degree (P<0.05) of association between the N. caninum serological status of dams and daughters. The seropositive conversion rate was estimated as 0.37%, 3.00% and 6.94% per 100 cow-years at Farms I, II and III, respectively. The seronegative conversion rate was estimated as 31.58% and 11.11% per 100 cow-years at Farms I and III, respectively. In all herds, there was no difference (P>0.05) in the culling rate between the cattle that were seropositive cattle and seronegative for N. caninum infection. The results from this study confirm the importance of vertical transmission in the epidemiology of N. caninum. Although a few positive seroconversions indicated horizontal transmission, it does not appear to be the major route of infection for N. caninum.     

A multiplex PCR for the detection of Brucella spp. and Leptospira spp. DNA from aborted bovine fetuses

Bovine brucellosis and leptospirosis are important causes of bovine abortion around the world. Both diseases can be serologically diagnosed, but many factors may cause false positive and negative results. Direct methods based on bacteriological isolation are usually employed, but they are difficult, time consuming and dangerous. Monoplex polymerase chain reaction (PCR) have been successfully described for the detection of Brucella spp. and Leptospira spp. Aiming at improvement in the direct diagnosis, a multiplex PCR (mPCR) for the detection of these agents in aborted bovine fetuses is described. The detection threshold of the mPCR was evaluated in experimentally contaminated bovine clinical samples using a conventional proteinase K/SDS or a boiling-based extraction protocols. The mPCR was applied to two groups of clinical samples: 63 episodes of bovine abortion and eight hamsters experimentally infected with Leptospira interrogans serovar pomona. Adopting microbiological isolation as reference, the test showed a sensitivity of 100% in both groups of clinical samples. Seven samples collected from bovine fetuses were Brucella spp. culture negative but showed positive results in mPCR. Regarding Leptospira spp. detection, similar results were observed in three bovine clinical samples. All hamsters infected with Leptospira were positive in both microbiological culture and mPCR. The boiling extraction protocol showed better results in some clinical samples, probably by the removal of PCR inhibitors by heat treatment. The high sensitivity, simplicity and the possibility of detection of both bacteria in a single tube reaction support the use of the mPCR described in the routine diagnosis.     

Influence of rubber trees on leaf-miner damage to coffee plants in an agroforestry system

The coffee leaf-miner (CLM) (Leucoptera coffeella Guérin-Mèneville; Lepidoptera: Lyonetiidae), the main pest of coffee plants, occurs widely throughout the Neotropics where it has a significant, negative economic and quantitative impact on coffee production. This study was conducted in a rubber tree/coffee plant interface that was influenced by the trees to a varying degrees depending on the location of the coffee plants, i.e. from beneath the rubber trees, extending through a range of distances from the edge of the tree plantation to end in a coffee monocrop field. The most severe damage inflicted on coffee plants by the CLM (number of mined leaves) from April, which marks the start of the water deficit period, until September 2003 was in the zone close to the rubber trees, whereas the damage inflicted on plants in the monocropped field was comparable to that on coffee plants grown directly beneath the rubber trees, which received about 25–40 % of the available irradiance (I_r—available irradiation at a certain position divided by the irradiation received in full sunlight, i.e. in the monocrop). From May until July damage caused by the CLM nearly doubled in each month. In midwinter (July), the damage decreased perceptibly from the tree edge toward the open field. From September onward, with the rising air temperatures CLM damage in the coffee monocrop started to increase. Based on these results, we conclude that coffee plants grown in the full sun incurred the most damage only at the end of winter, with warming air temperatures. Coffee plants grown in shadier locations (25–40 % I_r) were less damaged by the CLM, although a higher proportion of their leaves were mined. The rubber trees probably acted as a shelter during the cold autumn and winter seasons, leading to greater CLM damage over a distance outside the rubber tree plantation that was about equal to the height of the trees. Future studies should attempt to relate leaf hydric potential to pest attack in field conditions. More rigorous measurements of shade conditions could improve our understanding of the relationship of this factor to CLM attack.     

Feed restriction followed by realimentation in prepubescent Zebu females

In the present study, the effect of restricting the feed intake for 77 days and subsequent compensatory growth for 50 days of Sindi females were evaluated. Eighteen animals with an initial age of 21 months and a mean weight of 211.7 kg were placed into three groups according to the following alimentary regimens: feed ad libitum, feed restricted to 20 % dry matter, and feed restricted to 40 % dry matter. In the feed-restriction phase, the nutrient intake decreased (P?<?0.001) with an increase in the restriction level. As a consequence, the observed decrease in ingestion and serum concentrations of total protein, albumin and globulin, urea, glucose, calcium, and phosphorus were inversely proportional (P?<?0.001) to the restriction level. Significant differences in the nutrient intake and serum concentration were not observed in the realimentation phase (P?<?0.05). When animals in the control group reached the end of the feed-restriction phase, their weights (P?<?0.05) were similar to those in the 20 % restricted group, and both obtained a final weight that was greater than that of animals in the 40 % restricted group. In the feed-restriction phase, the control group had a similar mean daily weight gain (P?>?0.05) to animals in the 20 % restricted group and (P?<?0.05) 40 % restricted group. However, in the realimentation phase, the 40 % restricted group obtained greater weight gain rates (P?<?0.05), better food conversions, and partial compensatory gains. In particular, none of the restricted groups reached the final weight of the control group. In the feed-restriction phase, ingested nitrogen, nitrogen excreted in urine and feces, nitrogen balance and retained nitrogen decreased (P?<?0.05) with an increase in the restriction level. In the realimentation phase, none of the nitrogen balance variables were influenced by the restriction level (P?<?0.05). Females in the 40 % restricted group presented better food conversion rates and greater weight gains in the realimentation phase. Based on the animals’ compensatory weight gain, a feed-restriction rate of 20 and 40 % can be adopted as a nutritional management practice for prepubescent Sindi females.     

Phylogenetic and structural studies of a novel equine papillomavirus identified from aural plaques

Papillomaviruses (PVs) infect a wide range of animal species and show great genetic diversity. To date, excluding equine sarcoids, only three species of PVs were identified associated with lesions in horses: Equus caballus papillomavirus 1 (EcPV1-cutaneous), EcPV2 (genital) and EcPV3 (aural plaques). In this study, we identified a novel equine PV from aural plaques, which we designated EcPV4. Cutaneous samples from horses with lesions that were microscopically diagnosed as aural plaques were subjected to DNA extraction, amplification and sequencing. Rolling circle amplification and inverse PCR with specific primers confirmed the presence of an approximately 8 kb circular genome. The full-length EcPV4 L1 major capsid protein sequence has 1488 nucleotides (495 amino acids). EcPV4 had a sequence identity of only 53.3%, 60.2% and 51.7% when compared with the published sequences for EcPV1, EcPV2 and EcPV3, respectively. A Bayesian phylogenetic analysis indicated that EcPV4 clusters with EcPV2, but not with EcPV1 and EcPV3. Using the current PV classification system that is based on the nucleotide sequence of L1, we could not define the genus of the newly identified virus. Therefore, a structural analysis of the L1 protein was carried out to aid in this classification because EcPV4 cause lesion similar to the lesion caused by EcPV3. A comparison of the superficial loops demonstrated a distinct amino acid conservation pattern between EcPV4/EcPV2 and EcPV4/EcPV3. These results demonstrate the presence of a new equine PV species and that structural studies could be useful in the classification of PVs.