Single nucleotide polymorphism discovery of Pinus radiata with chromosome walking PCR method

In this paper, the basic principle of chromosome walking is presented and we used an actin gene of radiata pine (Pinus radiata) as an example to conduct upstream and downstream chromosome walking for EST sequences. The full genomic sequence (2154 bp) of the actin gene, including promoters 5′ UTR, CDS and 3′ UTR, was identified by chromosome walking. PCR amplification and DNA band sequencing from 200 unrelated radiata pine trees revealed a total of 21 SNPs for the actin gene, three in the promoter region, 15 in CDS and 4 in 3′ UTR. The results of this experiment provide a technical framework for SNPs discovery in none coding regions of candidate genes. __________ Translated from Acta Botanica Boreali-Occidentalia Sinica, 2007, 27 (8): 1571–1576 [译自: 西北植物学报]     

Gene for broad, contiguous dark stripes in cocozelle squash (Cucurbita pepo)

Alternating intense (dark) and light stripes on the fruits are a fairly common feature of Cucurbita pepo, a highly variable species encompassing various kinds of pumpkins, squash, and gourds. The intense stripes can be narrow and broken or broad and contiguous. Narrow, broken intense striping is conferred by allele l-1 ^St, which is dominant to allele l-1 for non-striped, lightly colored fruits and recessive to allele L-1 for non-striped, intensely colored fruits. Cocozelle-type squash often exhibit broad, contiguous intense stripes. The inheritance of this characteristic was studied by transferring it from cocozelle squash and preparing nearly isogenic lines having broad-striped, narrow-striped, and non-striped light-colored fruits. In the broad-striped near-isogenic line, the intense stripes averaged 37% wider than in its narrow-striped counterpart. The broad-striped line was crossed with the narrow-striped line, the non-striped light-colored line, and the non-striped intense-colored `Fordhook Zucchini'. Broad striping was dominant to narrow striping and to non-striped light and conferred by a single gene; it was recessive to non-striped intense. The gene for broad striping was found to be allelic to that for narrow striping and to that for non-stripe dintense and is herein assigned the symbol l-1 ^BSt. Dominance relationships at the l-1 locus were observed to be L-1>l-1 ^BSt >l-1 ^St >l-1. This revised version was published online in July 2006 with corrections to the Cover Date.     

Kinetic modeling of the thermal aggregation of patatin.

A kinetic model of the thermal aggregation of patatin is presented based on chromatographic analysis of the proportions of nonaggregated and aggregated patatin. It was observed that the decrease of the amount of nonaggregated patatin proceeded initially quickly and was followed by slower aggregation at longer incubation times. It was shown that this behavior was not due to heterogeneity of the starting material. It was noted that overestimation of the amount of native molecules after a heat treatment, caused by refolding of the unfolded protein during the cooling step prior to the analysis, was significant and could not be neglected. Hence, corrections based on information on the structural properties of patatin were applied. Taking this into account, a model was proposed consisting of a first-order formation of reactive particles, followed by a second-order aggregation reaction. This model described the thermal aggregation of patatin rather accurately and was confirmed by experiments at various protein concentrations.     

Thermal aggregation of patatin studied in situ.

In this work dynamic light scattering was used to study the thermal aggregation of patatin in situ, to elucidate the physical aggregation mechanism of the protein and to be able to relate the aggregation behavior to its structural properties. The dependence of the aggregation rates on the temperature and the ionic strength suggested a mechanism of slow coagulation, being both diffusion and chemically limited. The aggregation rate dependence on the protein concentration was in accordance with the mechanism proposed. The aggregation rates as obtained at temperatures ranging from 40 to 65 degrees C correlated well with unfolding of the protein at a secondary level. Small-angle neutron scattering and dynamic light scattering results were in good accordance; they revealed that native patatin has a cylindrical shape with a diameter and length of 5 and 9.8 nm, respectively.     

Effect of plant density in coupled aquaponics on the welfare status of African catfish,Clarias gariepinus

We investigated the effects of plant density on the welfare of African catfish, Clarias gariepinus, in coupled aquaponics over 85 days. The moderate density (mpd) of basil, Ocimum basilicum, was compared with the high density (hpd) and control (n = 0). The behavior was analyzed by visual and video observations, and after the application of induced stressors, skin injuries, blood glucose, lactate, and plasma cortisol responses were considered. The hpd fish showed the least activity (control: visual 77.8%, video 81.6%; mpd: 74.6%, 82.6%; hpd: 63.2% [p < 0.05], 78.8%). High agonistic behavior (control: 5, 131; mpd: 4, 57; hpd: 1, 45) and the highest number of injuries (control: 3.9; mpd: 2.9; hpd: 3.4) were observed in the control. Glucose and lactate levels did not differ significantly (control: 5.5, 2.6 mmol/L; mpd: 5.6, 2.7 mmol/L; hpd: 5.3, 2.6 mmol/L); however, cortisol levels did (control: 18.8 ng/mL, mpd: 19.9 ng/mL, hpd: 25.8 ng/mL). pH adjustment led to additional stress, resulting in temporal cortisol alterations. While in the control and mpd, low cortisol levels were followed by acute responses and downregulation, the hpd fish showed prior elevation and lagged an acute response. However, comparing injuries and behavioral patterns with control, aquaponics with high basil density influenced African catfish positively.     

Cell wall disruption: An effective strategy to improve the nutritive quality of microalgae in African catfish (Clarias gariepinus)

The rigid cell walls of microalgae may hinder their utilization in fish feeds. The current experiment assessed the correlation between the accessibility of microalgae nutrients and their in vivo digestibility in African catfish. Nannochloropsis gaditana biomass was subjected to physical or mechanical treatments to weaken its cell wall; untreated—no disruption treatment (UNT), pasteurization (PAS), freezing (FRO), freeze‐drying (FRD), cold pasteurization (L40) and bead milling (BEM). Six experimental diets formulated from differently treated and untreated microalgae (at 30% diet inclusion level) were tested on growth performance and apparent nutrient digestibility (ADCs) in juvenile African catfish. A basal diet (REF) containing no microalgae was used as reference diet. Results showed that biomass gain and feed conversion ratio of fish fed L40 and BEM diets increased by 13% and 11%, respectively, relative to the UNT diet. Additionally, FRD, FRO, L40 and BEM cell wall disruption treatments improved protein digestibility by 0.5%, 5.9%, 8.4% and 16.3%, respectively, compared to the UNT treatment. There was a positive correlation between accessibility of microalgal nutrients and their digestibility in African catfish. Nutrient digestibility of microalgae was dependent on extent of cell disruption. Also, the impact of cell disruption on nutrient digestibility of microalgae differs between African catfish and Nile tilapia.     

Pre‐Columbian fisheries catch reconstruction for a subtropical estuary in South America

Small‐scale fisheries provide food and livelihoods for thousands of people along the Brazilian coastline. However, considerable uncertainties still surround the extent to which artisanal and subsistence fisheries contribute to the total of national landings and their historical ecological significance. Fisheries monitoring is deficient in Brazil, and historical records are limited to irregular accounts spanning the last few decades, while this coastline has supported human populations for at least 6,000 years. Here, we estimate pre‐Columbian subsistence catches for a large subtropical estuary in southern Brazil. Our results suggest that prehistoric populations may have extracted volumes of fish biomass higher than or comparable with historical subsistence fisheries in the region, and that the latter is likely underestimated. If a long‐term perspective is required to evaluate the current economic value and status of fisheries in subtropical and tropical South America, this should go beyond the historical time interval and integrate the contribution of pre‐Columbian archaeology.     

Effect of fertilizers and irrigation on multi-configuration electromagnetic induction measurements

Electromagnetic induction (EMI) data are often used to investigate spatial and temporal patterns of soil texture, soil water content and soil salinity. We hypothesized that the EMI methodology might thus also offer potential to detect agricultural legacy effects originating from fertilizer application and irrigation of different fields. Therefore, we performed EMI measurements on two long-term field experiments (LTFE) at Thyrow near Berlin (Germany) that differed in agricultural management with regard to long-term irrigation in combination with mineral (NPK and lime) and organic amendments (straw and farmyard manure). Two different rigid-boom multi-coil EMI instruments were used to measure simultaneously the apparent electrical conductivity (ECa) over nine different depth ranges to study the entire soil profile from topsoil to deep subsoil. Additionally, soil samples were taken from the different treatments to ground-truth the measurements and disentangle the nutrient application or irrigation effects from natural soil heterogeneity. The soil samples indicated a rather homogenous soil and the correlation between soil parameters or states were not significant. However, the treatments showed significant differences in measured ECa values. In general, ECa values were largest on regularly irrigated as well as on mineral and organic fertilized plots, with regular irrigation exhibiting the largest impact on EMI records even though the last application was months before the EMI measurement. Overall, this study reveals that EMI data can support the classical in situ assessment of agricultural management effects within LTFE, while offering new potentials in detecting and understanding legacy effects of agricultural management on spatial soil properties at farm level.     

Effects of diet formulations containing proteins from different sources on intestinal colonization by Campylobacter jejuni in broiler chickens

The objective of this study was to compare the effects of 3 diet formulations containing different protein sources (animal, plant, and a combination of animal and plant) on the colonization of Campylobacter jejuni in the gastrointestinal tract of broiler chickens. A freshly isolated strain of C. jejuni (biotype IV, serotype HS O:21, O:29, HL untypable) from a broiler chicken was used to infect 3-day-old chicks that had been free of C. jejuni; 0.5 mL of an inoculum containing 10⁸ colony-forming units was administered orally. Shedding of the organism was studied, and C. jejuni in the ceca, jejuni, and crop were enumerated by quantitative culture. The isolates recovered from the birds during the study period of 35 d were characterized and confirmed as C. jejuni by the use of standard methods and underwent biotyping, serotyping, antimicrobial susceptibility testing by disk diffusion and the E-test, and flagellin gene typing. A cyclical pattern of shedding of C. jejuni was observed in all the birds. Colonization was highest in the ceca. The ceca of birds receiving plant-protein-based feed had significantly less colonization then the ceca of birds receiving the other types of feed, whereas the differences in colonization of the jejuni and crops were not significant. Characterization by biotyping, serotyping, and flagellin gene typing showed that 95% of the recovered isolates were identical to the strain used for infecting the chicks. However, with the Lior-HL typing scheme, 74% of the recovered isolates were HL untypable. Antimicrobial resistance testing did not reveal significant differences between the infecting strain and the recovered isolates among the different feed groups.