Universal PCR primers for ribosomal protein gene introns of fish

Human ribosomal protein (RP) gene sequences with respect to intron/exon structures and corresponding cDNA or genomic data of fish species were obtained from the GenBank database. Based on conserved exon sequences, 128 primer pairs for 41 genes were designed for exon-primed intron-crossing (EPIC) polymerase chain reaction (PCR). In reference to the draft genome sequences of the Pacific bluefin tuna (Thunnus orientalis), 12 primer pairs expected to amplify introns of the bluefin tuna with lengths of 500–1000 bp were selected and applied to six distantly related fish species belonging to the Orders Clupeiformes, Tetraodontiformes, Pleuronectiformes, Perciformes, Scorpaeniformes, and Anguilliformes. PCR amplification was observed for at least four species in each primer pair, and all fragments were larger than those expected for intronless amplification. Single fragment amplification was observed for at least seven primer pairs per species. Fragment sizes of the bluefin tuna for nine primer pairs corresponded to those expected from the genomic data. Thus, our primer pairs are potentially applicable to a wide variety of fish species and serve as an initial step for isolating single-copy nuclear DNA sequences.     

Effect of <Emphasis Type="Italic">Lactococcus lactis</Emphasis> K-C2 on the growth performance,amino acid content and gut microflora of amberjack <Emphasis Type="Italic">Seriola dumerili</Emphasis>

This study aimed to evaluate the effect of Lactococcus lactis K-C2 on the growth performance, microbial diversity, and release of free amino acids in the intestinal tract and the edible parts of young amberjack, Seriola dumerili. Fish were fed a diet with or without strain K-C2 (2?×?10¹⁰ cfu/g feed) for 25 days. The results indicated that the growth performance of fish in the treated group was significantly higher than those in the control group (p?<?0.05). The amount of five amino acids (aspartate, sarcosine, taurine, alanine, and arginine) in the gut content and 13 of 21 amino acids in the edible parts of fish in the treated group were significantly higher (p?<?0.05) than those in the control group. Sphingomonas, Propionibacterium, and Mycobacterium were observed in gut microflora of fish in both the control and treated groups. Staphylococcus and Kocuria were detected in one sample from the control and treated groups; Acinetobacter and Acidobacteria were found in one sample from the control group. L. lactis was only found in one sample in the treated group. In conclusion, the dietary administration of probiotic L. lactis stimulated growth, reduced feed consumption, and improved the nutritional value of cultured amberjack.     

Potato Facing Global Challenges: How,How Much,How Well?

This paper surveys issues and developments emerging from the keynotes and participants’ presentations during the 20th EAPR Triennial Conference, held in Versailles, France, in July 2017, and puts them into the perspective of the general theme of the meeting: potato facing global challenges. It reveals important and far-reaching innovations in many areas of potato research, including breeding (genomic selection, high-throughput phenotyping, genome editing), plant protection (biocontrol) and seed production, but also a general innovation approach that follows an incremental pathway (and maintains many existing lock-in situations), and favours substitution strategies over system re-conceptualisation and testing, however urgently needed these might be to achieve or improve the sustainability of potato production in the medium to long run. While the assets and importance of potato as both a wholesome food and an essential part of future worldwide food systems were once more evidenced and highlighted, the contributions also revealed (i) a growing dichotomy between research activities carried out in high-income vs in low- or moderate-income countries, respectively; (ii) some gaps in the assessment of the sustainability of potato production in the medium to long run (external inputs such as fertilisers or pesticides, land and energy use efficiency); and (iii) persistent weaknesses in the integration of individual solutions into complete, operational potato production systems. Some areas for future investigations are identified.     

Identification of genetic sources with attenuated <Emphasis Type="Italic">Tomato chlorosis virus</Emphasis>-induced symptoms in <Emphasis Type="Italic">Solanum</Emphasis> (section <Emphasis Type="Italic">Lycopersicon</Emphasis>) germplasm

The whitefly-transmitted Tomato chlorosis virus (ToCV) (genus Crinivirus) is associated with yield and quality losses in field and greenhouse-grown tomatoes (Solanum lycopersicum) in South America. Therefore, the search for sources of ToCV resistance/tolerance is a major breeding priority for this region. A germplasm of 33 Solanum (Lycopersicon) accessions (comprising cultivated and wild species) was evaluated for ToCV reaction in multi-year assays conducted under natural and experimental whitefly vector exposure in Uruguay and Brazil. Reaction to ToCV was assessed employing a symptom severity scale and systemic virus infection was evaluated via RT-PCR and/or molecular hybridization assays. A subgroup of accessions was also evaluated for whitefly reaction in two free-choice bioassays carried out in Uruguay (with Trialeurodes vaporariorum) and Brazil (with Bemisia tabaci Middle-East-Asia-Minor1—MEAM1?=?biotype B). The most stable sources of ToCV tolerance were identified in Solanum habrochaites PI 127827 (mild symptoms and low viral titers) and S. lycopersicum ‘LT05’ (mild symptoms but with high viral titers). These two accessions were efficiently colonized by both whitefly species, thus excluding the potential involvement of vector-resistance mechanisms. Other promising breeding sources were Solanum peruvianum (sensu lato) ‘CGO 6711’ (mild symptoms and low virus titers), Solanum chilense LA1967 (mild symptoms, but with high levels of B. tabaci MEAM1 oviposition) and Solanum pennellii LA0716 (intermediate symptoms and low level of B. tabaci MEAM1 oviposition). Additional studies are necessary to elucidate the genetic basis of the tolerance/resistance identified in this set of Solanum (Lycopersicon) accessions.     

Sample size and power determination for detecting interactions in mixtures of chemicals

In the analysis of mixtures of drugs/chemicals it is often of interest to test for the presence of interaction. If the hypothesis of no interaction (additivity) is not rejected, then the analyst may reasonably claim additivity if and only if the study is powered to a desired (e.g., biologically meaningful) level. The objective of this article is to address the sample size and power issues related to testing the hypothesis of additivity at specified mixture points. The study of disinfectant by-products (DBPs) found in drinking water, described in earlier literature, is used to illustrate the procedures for estimating power and sample sizes for detecting interactions at specified mixtures. The four trihalomethanes used in the study are bromodichloromethane (BDCM), chlorodibromomethane (CDBM), chloroform (CHCl₃), and bromoform (CHBr₃)     

Hydraulic Retention Time Influence on Improving Flocculation in the Activated Sludge Processes Through Polyelectrolytes

Hydraulic retention time (HRT) influence improving sludge flocculation with adding the polyelectrolytes (non-ionic, anionic, and cationic) was studied on an activated sludge (AS) system fed with synthetic domestic wastewater (SDW), dairy industry wastewater (DIW), and caramel industry wastewater (CIW). The sludge volumetric index, food/microorganism ratio (F/M), and mixed liquor volatile suspended solids at different HRTs (6, 8 and 10 h) were monitored on an experimental model. Results showed that both SDW and IW had the best sludge flocculation conditions at 8 h and 100 mL of non-ionic polyelectrolyte (0.2 mg L^?1). In addition, this phenomenon reached the organic matter removal efficiencies of 95.9, 95.7, and 94.2% for SDW, DIW, and CIW, respectively. Therefore, optimum HRT increased the organic matter removal efficiencies by 10%, sludge concentration by 37% (22–55%), and F/M ratio by 70%. Moreover, the polyelectrolytes used in AS improved the sludge flocculation by 2.9 times.     

Effects of seasonal and environmental changes on aquaculture production in tropical Lake Volta,Ghana

Globally, aquaculture production is faced with numerous challenges, notable among which is water quality. The study determined seasonal environmental changes in Lake Volta and its implications on cage production of Nile tilapia, Oreochromis niloticus in experimental and commercial farm (Sun Woo Farm) set-ups. For each set-up, three cages were used, each measuring 81 and 162.5 m³ for experimental and commercial, respectively. The cages were stocked with 22.5 g fingerlings at a rate of 40 and 80 m^?3 in experimental and commercial cages, respectively, and fed commercial diet. The growth performance, yield, economics, and selected water quality parameters were monitored during the dry and wet seasons between November 2014 and July 2015. There were no differences in water quality parameters between dry and wet seasons (p?>?0.05). Water quality for both seasons remained within limits required for good Tilapia growth in both set-ups. There were minimal variations in growth characteristics between seasons which were not significant; however, final mean weight and yields were high in the dry seasons in both set-ups. The cost of feed and fingerling accounting for about 80% of total costs were the major components identified to affect cost of production. A higher profit index and returns on investment were observed in the dry season in both set-ups and was linked to higher survival rates in the season. Production of Nile tilapia in cages can be cultured throughout the year without any adverse effects as exhibited in similar production patterns in both experimental and commercial set-ups.     

Within-stem variations in mechanical properties of <Emphasis Type="Italic">Melia azedarach</Emphasis> planted in northern Vietnam

Within-stem variations in the mechanical properties of 17–19-year-old Melia azedarach planted in two sites in northern Vietnam were examined by destructive and nondestructive methods. Wood samples were collected from 10, 50, and 90% of the radial length from pith on both sides (North and South) at 0.3, 1.3, 3.3, 5.3, and 7.3 m heights above the ground. The mean values in whole trees of wood density (WD), modulus of rupture (MOR), modulus of elasticity (MOE), and dynamic modulus of elasticity (E_d) at 12% moisture content were 0.51 g/cm³, 78.58 MPa, 9.26 GPa, and 10.93 GPa, respectively. Within the stem, the radial position was a highly (p?<?0.001) significant source of variation in mechanical properties. MOR, MOE, and E_d increased from pith to bark. WD had a strong positive linear relationship with both MOR (r?=?0.85, p?<?0.001) and MOE (r?=?0.73, p?<?0.001). This suggests that it is potentially possible to improve mechanical properties through controlling WD. MOR had also a strong linear relationship with E_d (r?=?0.84, p?<?0.001). This indicates that E_d is a good indicator to predicting the strength of wood if the density of measured element is known. Besides, the stress wave method used in this study provides relatively accurate information for determining the stiffness of Melia azedarach planted in northern Vietnam.     

Neutral models for testing landscape hypotheses

Neutral landscape models were originally developed to test the hypothesis that human-induced fragmentation produces patterns distinctly different from those associated with random processes. Other uses for neutral models have become apparent, including the development and testing of landscape metrics to characterize landscape pattern. Although metric development proved to be significant, the focus on metrics obscured the need for iterative hypothesis testing fundamental to the advancement of the discipline. We present here an example of an alternative neutral model and hypothesis designed to relate the process of landscape change to observed landscape patterns. The methods and program, QRULE, are described and options for statistical testing outlined. The results show that human fragmentation of landscapes results in a non-random association of land-cover types that can be describe by simple statistical methods. Options for additional landscape studies are discussed and access to QRULE described in the hope that these methods will be employed to advance our understanding of the processes that affect the structure and function in human dominated landscapes.     

Geospatial delineation of South Korea for adjusted barley cultivation under changing climate

Determining effective measures to alleviate the impact of climate change on crops under various regional environments is one of the most urgent issues facing agriculture. In this study, geographic regions of South Korea for future-adjusted barley cultivation were outlined and the impact of climate change on barley production in the next 100 years was evaluated under two greenhouse gas concentration trajectory scenarios: the representative concentration pathway (RCP) 4.5 and RCP 8.5. To achieve our intended study goals, a geospatial crop simulation modeling (GCSM) scheme was formulated using CERES-barley model of Decision Support System for Agricultural Technology (DSSAT) crop model package version 4.6 to simulate grid-based geospatial crop yields. Two experiments were carried out at an open field to obtain model coefficients for the nation and at temperature gradient field chambers to evaluate the performance of the CERES-barley model under elevated temperature conditions. Suitable cultivation regions for three different types of barley (naked, hooded, and malting) under changing climate were projected to expand to the northern regions under both RCP 8.5 and RCP 4.5. However, they were projected to expand more rapidly under RCP 8.5 than those under RCP 4.5. Projected yields of four barley varieties were increased with a slow phase as year progressed under RCP 4.5 scenario. However, they were rapidly increased under RCP 8.5 scenario. It appears that geospatial variation in barley yield under changing climate can be effectively outlined. Therefore, GCSM system might be useful for determining impacts of climate change on geospatial variations of crops, potentially providing means to impede food insecurity.