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.     

Growth, Condition, and Size Distribution of Paddlefish, Polyodon spathula, Juveniles Reared in Ponds at Three Densities

Abstract.— A study was conducted to determine the effect of increasing density on growth and size distribution of paddlefish, Polyodon spathula, juveniles reared in ponds. Feed‐trained paddlefish of mean weight (±SE) 25.8 ± 1.1 g were randomly stocked into nine 0.02‐ha ponds at 12,355, 18,533, and 24,710 paddlefish/ha, three replications per treatment. The fish were fed daily in excess of what they would eat for 97 d, beginning with a floating trout diet containing 45% protein and 16% lipid and then transferring to a floating catfish diet containing 32% protein and 4.5% lipid. Survival at harvest was not significantly different (P > 0.05) among treatments and averaged 90%. Mean final weights (±SD) for the low‐, middle‐, and high‐density treatments were 205.2 ± 54.1, 174.8 ± 53.2, and 178.6 ± 51.4 g, respectively. Best‐fit distributions centered on these means were lognormal. The low‐density distribution was significantly different (P < 0.05) from the two higher densities, which were not significantly different from each other (P > 0.05). Paddlefish weight at the minimum target length of 35 cm was estimated to be 100 g by regression analysis. The probability of paddlefish reaching or exceeding 100 g was 90% for the low‐density treatment. For the two higher densities, probabilities were 79 and 78%, respectively. Mean Fulton’s condition factors (FCFs) (±SD) were 250 ± 19, 242 ± 4, and 256 ± 37 for the low‐, middle‐, and high‐density treatments, respectively. The FCF for the middle‐density treatment was significantly lower than for the low‐ and high‐density treatments (P < 0.05), which were not significantly different from each other (P > 0.05). CV, feed conversion ratio, and relative growth were not significantly different (P > 0.05) among treatments and averaged 0.43, 1.50, and 5.45, respectively. Monoculture of paddlefish juveniles in ponds results in a hierarchic size structure when density is at least greater than 12,355 paddlefish/ha. The effect is enhanced with increasing density but becomes asymptotic as density approaches 18,533 paddlefish/ha. Feeding in excess does not ameliorate the effect.     

Use of spectral radiance for correcting nitrogen deficiencies and estimating soil test variability in an established bermudagrass pasture

The use of variable rate technology has become increasingly popular for applying plant nutrient elements. The most widely used method for determining variable fertilizer rates is presently based on soil testing and yield mapping. Three field studies (Bumeyville 1995, Burneyville 1996, and Ardmore 1996) were initiated in established Midland bermudagrass [Cynodon dacrylon (L) Pers.] pastures to determine the relationship between spectral radiance at specific wavelengths with forage nitrogen (N) removal and biomass, and to determine field variability of soil test parameters. Variable N (applied to 1.5 × 2.4 m subplots within 2.4 × 45.7 m main plots), fixed N and check treatments were evaluated at each location. Spectral radiance readings were taken in the red (671±6 nm), green (570±6 nm), and near infrared (NIR) (780±6 nm) wavelengths. The normalized difference vegetation index (NDVI) was calculated as NIR‐red/NIR+red. Variable N rates were applied based on NDVI. The highest fixed variable N rate was set at 224, 336, and 672 kg N ha^‐1 for Burneyville, 1995, 1996, and Ardmore, 1996, respectively. At Bumeyville, soil samples were collected in all variable rate plots (1.5 × 2.4 m) and analyzed for various soil test characteristics. NDVI, red, green, and NIR spectral radiance readings were correlated with bermudagrass forage N removal and yield. Correlation of forage yield and N removal with red, NIR, and NDVI were best with maximum forage production, however, when forage production levels were low correlation decreased dramatically for the red wavelength compared with NIR and NDVI. Forage yield and forage N removal in variable rate treatments increased when compared to the check while being equal to the half‐fixed and fixed rates where higher N rates were applied. Also, variability about the mean in variable rate plots was significantly lower than half‐fixed and fixed rates which supports adjusting N rates based on indirect NDVI measurements. Variable N rate plots reduced fertilizer inputs by 60% and produced the same yield as fixed rate plots, while fixed and half‐fixed rates did not increase N content in the forage over that of the variable rate treatment. Soil sample data collected from small consecutive plots (<4 m²) was extremely variable indicating that intense sampling would be needed if variable fertilizer application were to be based on soil test results.     

The Compostable Plastic Poly(lactic) Acid Causes a Temporal Shift in Fungal Communities in Maturing Compost

The compostable biopolymer, poly(lactic) acid (PLA), is increasingly being used as an alternative to conventional plastics for short shelf-life products, disposable bags and packaging, and in agriculture. Despite the increase in the amount of PLA entering composting systems, few studies have examined the impact of PLA degradation on the compost microbial community. Thermophilic fungi play an import role in the composting process as they secrete hydrolytic enzymes capable of breaking down an array of complex natural polymers. In this study, the impact of PLA hydrolysis on the compost fungal community was examined by terminal restriction fragment length polymorphism and 454 sequencing. At 25°C, the effect of PLA on the surrounding compost community was relatively small and no physical changes were observed to the PLA films. However, when incubated at 50°C, where physical disintegration of PLA was occurring, a clear divergence between the compost populations in the presence and absence of PLA was evident after 2 months but became closer to the population in the absence of PLA after 4 months indicating that, after causing an initial perturbation after 2 months, the population began to return to that seen in the absence of PLA. The only exception was in the population containing 50% (w/w) PLA film, which remained divergent after 4 months and was associated with a marked acidification of the compost. Thus, 454-pyrosequencing revealed that the presence of PLA caused a strong selection for a Thermomyces sp. that was present only at low abundance in the absence of PLA.     

Carbon isotopic ratios of wetland and terrace soil sequences in the Maya Lowlands of Belize and Guatemala

This article provides new data and synthesizes earlier findings on the carbon isotope ratios of the humin part of soil organic matter from a range of sites in the central Maya Lowlands. Changes down the soil profile in carbon isotope ratios can provide an important line of evidence for vegetation change and erosion over time, especially in well dated aggrading profiles. Research thus far has provided substantial evidence for significant inputs from C₄ vegetation in buried layers from the Ancient Maya periods in depositional soils but equivocal evidence from sloping soils. We present new findings from soil profiles through ancient Maya wetland fields, upland karst wetlands, ancient Maya aguadas (reservoirs), and ancient Maya terraces. Most of the profiles exhibited δ¹³C enrichment greater than the 2.5–3‰ typical from bacterial fractionation. Seven of nine ancient Maya wetland profiles showed δ¹³C enrichment ranging from 4.25 to 8.56‰ in ancient Maya-dated sediments that also contained phytolith and pollen evidence of grass (C₄ species) dominance. Upland karst sinks and ancient reservoirs produced more modest results for δ¹³C enrichment. These seasonal wetland profiles exhibited δ¹³C enrichment ranging from 1 to 7.3‰ from the surface to ancient Maya-period sediments. Agricultural terraces produced mixed results, with two terraces having substantial δ¹³C enrichment of 5.34 and 5.66‰ and two producing only equivocal results of 1.88 and 3.03‰ from modern topsoils to Maya Classic-period buried soils. Altogether, these findings indicate that C₄ plants made up c. 25% of the vegetation at our sites in the Maya Classic period and only a few percent today. These findings advance the small corpus of studies from ancient terraces, karst sinks, and ancient wetland fields by demonstrating substantial δ¹³C and thus C₄ plant enrichment in soil profile sections dated to ancient Maya times. These studies are also providing a new line of evidence about local and regional soil and ecological change in this region of widespread environmental change in the Late Holocene.     

Primary and secondary metabolite composition of kernels from three cultivars of Portuguese chestnut (Castanea sativa Mill.) at different stages of industrial transformation

Chestnut (Castanea sativa) is an important basic food in rural diets and a major starch crop used in a similar way to potatoes. Chestnuts are a fundamental economic resource in the "chestnut regions" not only for the fruit but also for the chestnut wood. Chestnuts have become increasingly important with respect to human health, for example, as an alternative gluten-free flour source. Chestnuts are also a rich source of other beneficial compounds, but there have been few studies on the composition during processing. In this study, we analyzed the chemical composition of three Portuguese cultivars at different stages of industrial processing. The chestnut cultivars were Longal, Judia, and Martaínha. All three cultivars had high moisture contents but were low in ash, crude fat, and crude protein contents, with high starch and low fiber contents. The free amino acid contents, including various essential amino acids, varied depending on the cultivar. All three cultivars also had a significant content of polyphenolics with gallic acid; ellagic acid was predominant among hydrolyzable and condensed tannins. Many of these compounds are known to exert significant positive effects on human health. The one-way analysis of variance for fresh chestnut shows significant differences among the three cultivars for most of the studied parameters. The same statistical analysis applied to each one of the two cultivars (Judia and Longal) sampled for the four processing steps analyzed indicates a significant effect of this factor in practically all of the constituents. On the other hand, the two-way analysis of variance shows that, besides the residual, the processing step and the interaction cultivar x processing step were the factors that more contributed for the total variation observed in the constituents analyzed, while the contribution of cultivar was much less significant.     

Extraction of newly immobilized n from an illinois mollisol using aqueous phenol

Studies were conducted on an ¹⁵N-enriched Illinois Mollisol (Flanagan silt loam) to determine the extractability of newly immobilized N with aqueous phenol (45%, v/v). In comparison to mild extradants proposed as indexes of plant available N (i.e. 10 mw NaHCO₃ and hot 10 m CaCl₂), phenol showed the highest selectivity for the immobilized N, both with regard to the amount of biomass N extracted and the magnitude of the extractability ratio (ER). Aqueous phenol was also more selective in removing the immobilized N than reagents used for extraction of soil organic matter (i.e. 150 m Na₄P₂O₇ and 100 m KOH). Results with soils incubated for up to 120 days showed that the amount of ¹⁵N extracted with aqueous phenol fluctuated with time and was related to changes in the soil microbial population, e.g. ER was highest when the bacterial population was maximal. Aqueous phenol shows promise as a selective extradant of potentially-available (labile) organic N in soils.     

Inter‐specific variability in organic nitrogen uptake of three temperate grassland species

We tested the inter‐specific variability in the ability of three dominant grasses of temperate grasslands to take up organic nitrogen (N) in the form of amino acids in soils of differing fertility. Amino acid uptake was determined by injecting dual labeled glycine‐2‐¹³C‐¹⁵N into the soil, and then measuring the enrichment of both ¹³C and ¹⁵N in plant tissue after 50 hours. We found enrichment of both ¹³C and ¹⁵N in root and shoot material of all species in both soils, providing first evidence for direct uptake of glycine. We show that there was considerable inter‐specific variability in amino acid uptake in the low fertility soil. Here, direct uptake of amino acid was greater in the grass Agrostis capillaris, which typically dominates low fertility grassland, than Lolium perenne, which inhabits more fertile sites. Direct uptake of amino acid for Holcus lanatus. was intermediate between the above two species. Unlike in the low fertility soil, there was no difference in uptake of either ¹³C or ¹⁵N by grasses in the high fertility soil, where uptake of mineral N is thought to be the major mechanism of N uptake of these grasses. Overall, our findings may contribute to our understanding of differences in competitive interactions between grasses in soils of different fertility status.     

利用ECMWF再分析数据验证PRECIS对中国区域气候的模拟能力

本文利用1979～1983年的ECMWF再分析数据作为准观测侧边界条件驱动Hadley气候预测和研究中心的区域气候模式系统PRECIS，验证PRECIS对中国区域的气候模拟能力。选择典型的观测站点北京模拟的日最高，最低气温、太阳短波总辐射和月均降水量与观测结果进行直接比较，显示：PRECIS具有很强的模拟地面气候季节变化的能力。全国740个台站的观测与模拟值的统计分析表明：尽管模拟的最高，最低气温在0℃附近有一‘锯齿’状的偏差，PRECIS能够很好地模拟全国范围最高，最低气温的型态分布特征；从全国范围看，模拟的降水值偏高，但显示出很强的模拟极端降水事件的能力；模拟的地面太阳短波总辐射与全国122个台站的观测结果的比较显示：PRECIS模拟的辐射值偏高，全国范围内约高22％。因此，当应用PRECIS输出结果进行气候变化的影响评价时，需要对模式的输出结果进行订正。