Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations

Background  

The establishment of mutant populations together with the strategies for targeted mutation detection has been applied successfully to a large number of organisms including many species in the plant kingdom. Considerable efforts have been invested into research on tomato as a model for berry-fruit plants. With the progress of the tomato sequencing project, reverse genetics becomes an obvious and achievable goal.     

Sodicity and salinity in a Brazilian Oxisol cultivated with sugarcane irrigated with wastewater

Changes in soil sodicity-salinity parameters are one of the most characteristic alterations after treated sewage effluent (TSE) irrigation in agro-systems. Considering the importance of these parameters for agricultural management, as well as the economical value of sugarcane for Brazil, the present study aimed at evaluating effects on soil sodicity and salinity under tropical conditions over 16 months of TSE irrigation in a sugarcane plantation at Lins, São Paulo State, Brazil. Soil samplings were carried out in February 2005 (before planting), December 2005 (after 8 months of TSE irrigation) and September 2006 (after 16 months of TSE irrigation) following a complete block design with four treatments and four replicates. Treatments consisted of: (i) control, without TSE irrigation; (ii) T100, T150 and T200, with TSE irrigation supplying 100% (0% surplus, total of 2524 mm), 150% (50% surplus, total of 3832 mm) and 200% (100% surplus, total of 5092 mm) of crop water demand, respectively. Compared to initial soil conditions, at the end of the experiment increases of exchangeable sodium (from 2.4 to 5.9 mmol_c kg⁻¹), exchangeable sodium percentage (ESP) (from 8 to 18%), soluble Na (from 1.4 to 4.7 mmol L⁻¹) and sodium adsorption ratio (SAR) of soil solution (from 3.6 to 12.6 (mmol L⁻¹)^0.5) were found in the soil profile (0-100 cm) as an average for the irrigated plots due to high SAR of TSE. Associated with the increments were mostly significant increases in clay dispersion rates at depths 0-10, 10-20 and 20-40 cm. Electrical conductivity (EC) of soil solution increased during the TSE irrigation period whereas at the end of the experiment, after short term discontinuation of irrigation and harvest, EC in the topsoil (0-10 and 10-20 cm) decreased compared to the previous samplings. Moreover, despite increasing sodicity over time mainly insignificant differences within the different irrigated treatments were found in December 2005 and September 2006. This suggests that independent of varying irrigation amounts the increasing soil sodicity over time were rather caused by the continuous use of TSE than by its quantity applied. Moreover, also plant productivity showed no significant differences within the TSE irrigated plots. The study indicates that monitoring as well as remediation of soil after TSE irrigation is required for a sustainable TSE use in order to maintain agricultural quality parameters.     

Irrigation scheduling strategies for cotton to cope with water scarcity in the Fergana Valley, Central Asia

The Central Asian countries face high water scarcity due to aridity and desertification but excess water is often applied to the main irrigated crops. This over-irrigation contributes to aggravate water scarcity problems. Improved water saving irrigation is therefore required, mainly through appropriate irrigation scheduling. To provide for it, after being previously calibrated and validated for cotton in the Fergana region, the irrigation scheduling simulation model ISAREG was explored to simulate improved irrigation scheduling alternatives. Results show that using the present irrigation scheduling a large part of the applied water, averaging 20%, percolates out of the root zone. Several irrigation strategies were analyzed, including full irrigation and various levels of deficit irrigation. The analysis focused a three-year period when experiments for calibration and validation of the model were carried out, and a longer period of 33 years that provided for an analysis considering the probabilities of the demand for irrigation water. The first concerned a wet period while the second includes a variety of climatic demand conditions that provided for analyzing alternative schedules for average, high and very high climatic demand. Results have shown the importance of the groundwater contribution, mainly when deficit irrigation is applied. Analyzing several deficit irrigation strategies through the respective potential water saving, relative yield losses, water productivity and economic water productivity, it could be concluded that relative mild deficits may be adopted. Contrarily, the adoption of high water deficit that produce high water savings would lead to yield losses that may be economically not acceptable.     

Feeding responses of juvenile shrimp Litopenaeus vannamei (Boone) fed at different frequencies under laboratory conditions

In shrimp farms, food partitioning during the course of the day is contradictory, ethology studies may help in determining the proper frequency. Litopenaeus vannamei juveniles were placed in 30 L aquariums (41 m⁻²), exposed to a 12:12 h light–dark cycle. Feeding was provided at 10% of biomass three, four and seven times per day, with observations made in 15 min h⁻¹ windows, initiated after the ration was offered. Latency to access the feeding tray and to start eating was recorded using instantaneous focal sampling and digestive tract filling (DTF) by the continuous focal method. Weight gain was recorded at the end of the experiment. We performed seven repetitions, with 28 individuals observed for 33 days for each treatment (490 h of observation). The three-times offering induced less latency for accessing the tray and for ingesting the feed as well as a higher DTF when compared with the other frequencies. Animals fed three and four times had similar weight gains, and were greater than those fed seven times. Our results indicate that a more spaced food offering stimulates the search for and ingestion of feed. As compared with other frequencies, the three-times-per-day option assumes lower labour costs and a more efficient use of the feed.     

Trawling for cephalopods off the Portuguese coast—Fleet dynamics and landings composition

Fleet dynamics was addressed for three cephalopod taxa of commercial interest, the squid Loligo vulgaris, the octopuses Octopus vulgaris and Eledone cirrhosa, and the cuttlefish Sepia officinalis, for 48 trawlers of the fish trawling fleet. Landing profiles (LP) were identified based on the species composition of the landings using hierarchical cluster analysis. Four out of a total of 12 different LP were related to cephalopods and other species associated with them.The effects on the landing proportions of a number of variables, year, season and vessel, are analysed for each of the species studied using generalized linear models (GLM). The factor “vessel”, including an ensemble of technical characteristics as well as the abilities of individual skippers, explained most of the model deviance, strongly reinforcing the existence of a fleet component dedicated to catch cephalopods. However, time also explains much of the variation found in the data.Seasonal alternation between landings of octopodidae and cuttlefish was observed within a small group of old trawlers operating mainly off the south coast, following the abundance cycles of these species. For a larger group of more modern trawlers, operating off the western coast, inter-annual shift between octopus and squid was found, together with a well marked seasonal pattern between the catches of cephalopods and horse mackerel.Spatial patterns of activity were identified using vessel monitoring system (VMS) data available for trawlers in Portugal, demonstrating the existence of cephalopod targeting strategies in Portuguese fish trawling activities.     

Salmonid fish viruses and cell interactions at early steps of the infective cycle

A flow cytometric virus-binding assay that directly visualizes the binding and entry of infectious pancreatic necrosis virus (IPNV), infectious haematopoietic necrosis virus (IHNV) and virus haemorrhagic septicaemia virus (VHSV) to several cell lines was established. The highest efficiency of binding was shown by the BF-2 cell line and this was used to study, at the attachment level, the interactions of these cells with salmonid fish viruses in coinfections, and to further determine if the earliest stage of the viral growth cycle could explain the previously described loss of infectivity of IHNV when IPNV is present. Our results demonstrated that IPNV binds to around 88% of cells either in single or dual infections, whereas IHNV attachment always decreased in the presence of any of the other viruses. VHSV binding was not affected by IPNV, but coinfection with IHNV reduced the percentage of virus-binding cells, which suggests competition for viral receptors or co-receptors. Internalization of the adsorbed IHNV was not decreased by coinfection with IPNV, so the hypothetical competence could be restricted to the binding step. Treatment of the cells with antiviral agents, such as amantadine or chloroquine, did not affect the binding of IPNV and VHSV, but reduced IHNV binding by more than 30%. Tributylamine affected viral binding of the three viruses to different degrees and inhibited IPNV or IHNV entry in a large percentage of cells treated for 30 min. Tributylamine also inhibited IHNV cytopathic effects in a dose-dependent manner, decreasing the virus yield by 4 log of the 50% endpoint titre, at 10 mm concentration. IPNV was also inhibited, but at a lower level. The results of this study support the hypothesis that IHNV, in contrast to VHSV or IPNV, is less efficient at completing its growth cycle in cells with a simultaneous infection with IPNV. It can be affected at several stages of viral infection and is more sensitive to the action of antiviral compounds.     

Nutrients removed by Kappaphycus alvarezii (Rhodophyta, Solieriaceae) in integrated cultivation with fishes in re-circulating water

The potential of the red alga Kappaphycus alvarezii to remove nutrients was tested to treat effluents of Trachinotus carolinus fish cultivation, and the production of carrageenan in this condition was analyzed. Experiments were conducted in four tanks of 8000 L with approximately 1200 fishes of 30 g each integrated with three tanks of 100 L with 700 g of K. alvarezii, as initial biomass per tank. Seawater was re-circulated between tanks with seaweed and with fish. As a control, three tanks with seawater circulating in an open system were utilized. Seawater samples were collected daily for 10 days and concentrations of nitrate, nitrite, ammonium and phosphate were determined in the inflow and outflow water of the tanks. Significant differences between both collecting points were considered as nutrient removal by the seaweed. Growth rates and carrageenan yields were also analyzed in seaweed cultivated in seawater and in effluents. Growth rates of seaweed cultivated in tanks were lower than those obtained in open sea and in laboratory cultivation. Effluents had concentrations of nitrate and nitrite ca. 100 times higher than in the control. Maximum values of nutrient removal on effluents were: nitrate = 18.2%; nitrite = 50.8%; ammonium = 70.5% and phosphate = 26.8%. All plants survived throughout the experimental period, but some developed “ice–ice”, a disease associated with physiological stress. After the experimental period, some plants selected and cultivated in open sea presented higher growth rates in 40 days, indicating nutrient storage. No significant differences between carrageenan yields of K. alvarezii cultivated in seawater and in the effluents were observed. Our results show that K. alvarezii can be utilized as a biofilter for fish cultivation effluents, reducing the eutrophication process and can also be processed for carrageenan production, which provides an additional benefit to the fisheries.     

Irrigation of paddy soil with industrial landfill leachate: impacts in rice productivity,plant nutrition,and chemical characteristics of soil

Treated industrial effluents have high levels of nutrients and dissolved organic matter. The irrigation of rice by flooding can increase nutrient uptake and grain yield. Therefore, this study evaluated the nutrient contents in the shoots and grain of the rice crop and also the chemical of the soil after irrigation of the crop with leachate of the treated industrial effluent. A greenhouse experiment was conducted using pots filled with 20 kg of soil in a randomized block design with three replications. The treatments consisted of control (irrigation with distilled water) and four concentrations of the leachate (25, 50, 75, and 100 %) for irrigation. At the end of the experiment, the nutrient contents in tissues of rice plants, sterility of spikelets, and grain mass were evaluated. Results showed that irrigation with the leachate at 25 % content increased the macro- and micronutrients’ concentrations in the shoot biomass and grain, except for potassium and iron. Irrigation with the industrial leachate decreased tillering and grain yield; however, it increased chlorophyll content, sterility of spikelets, and sodium intake at this leachate concentration. The potassium and sodium levels and the electrical conductivity values of soils irrigated with treated industrial leachate were increased. The use of the treated leachate from industrial effluents is an alternative that reuses the nutritional load, but the volume of leachate should be limited and monitored to prevent the sodicity in the soil and problemsdue to eutrophication.     

Two reported cytotypes of the emergent orchid model species <Emphasis Type="Italic">Erycina pusilla</Emphasis> are two different species

Each species is characterized by a specific set of chromosomes, which is described as the chromosome portrait or karyotype. In general, such a karyotype is the same for all individuals in the population. An exception to that rule has recently been found in the orchid Erycina pusilla, which has been reported to have two cytotypes with chromosome numbers of 2n = 10 and 2n = 12. Here, we examined the karyotypes of the two cytotypes and found differences in arm ratios and heterochromatin patterns as well as in the presence of satellite chromosomes and in the number and location of rDNA and telomeric repeat sites. These differences are extensive and would have required multiple chromosome rearrangements to generate the differences between the two karyotypes. We also found that F1 hybrids between the parents with the two different chromosome numbers resulted in sterile offspring, in accordance with our previous findings. The combination of hybrid sterility and extensively rearranged chromosomes supports the hypothesis that these two reported cytotypes are, in fact, two different species.