Using unsupervised learning techniques to assess interactions among complex traits in soybeans

Soybean yield components and agronomic traits are connected through physiological pathways that impose tradeoffs through genetic and environmental constraints. Our primary aim is to assess the interdependence of soybean traits by using unsupervised machine learning techniques to divide phenotypic associations into environmental and genetic associations. This study was performed on large scale, jointly analyzing 14 quantitative traits in a large multi-parental population designed for genetic studies. We collected phenotypes from 2012 to 2015 from a soybean nested association panel with 40 families of approximately 140 individuals each. Pearson and Spearman correlations measured phenotypic associations. A multivariate mixed linear model provided genotypic and environmental correlations. To evaluate relationships among traits, the study used principal component and undirected graphical models from phenotypic, genotypic, and environmental correlation matrices. Results indicate that high phenotypic correlation occurs when traits display both genetic and environmental correlations. In genetic terms, length of reproductive period, node number, and canopy coverage play important roles in determining yield potential. Optimal grain yield production occurs when the growing environment favors faster canopy closure and extended reproductive length. Environmental associations found among yield components give insight into the nature of yield component compensation. The use of unsupervised learning methods provides a good framework for investigating interactions among various quantitative traits and defining target traits for breeding.     

Antioxidant capacity, vitamin C, phenolics, and anthocyanins after fresh storage of small fruits.

Fresh strawberries (Fragaria x ananassa Duch.), raspberries (Rubus idaeus Michx.), highbush blueberries (Vaccinium corymbosum L.), and lowbush blueberries (Vaccinium angustifolium Aiton) were stored at 0, 10, 20, and 30 degrees C for up to 8 days to determine the effects of storage temperature on whole fruit antioxidant capacity (as measured by the oxygen radical absorbing capacity assay, Cao et al., Clin. Chem. 1995, 41, 1738-1744) and total phenolic, anthocyanin, and ascorbate content. The four fruit varied markedly in their total antioxidant capacity, and antioxidant capacity was strongly correlated with the content of total phenolics (0.83) and anthocyanins (0.90). The antioxidant capacity of the two blueberry species was about 3-fold higher than either strawberries or raspberries. However, there was an increase in the antioxidant capacity of strawberries and raspberries during storage at temperatures >0 degrees C, which was accompanied by increases in anthocyanins in strawberries and increases in anthocyanins and total phenolics in raspberries. Ascorbate content differed more than 5-fold among the four fruit species; on average, strawberries and raspberries had almost 4-times more ascorbate than highbush and lowbush blueberries. There were no ascorbate losses in strawberries or highbush blueberries during 8 days of storage at the various temperatures, but there were losses in the other two fruit species. Ascorbate made only a small contribution (0.4-9.4%) to the total antioxidant capacity of the fruit. The increase observed in antioxidant capacity through postharvest phenolic synthesis and metabolism suggested that commercially feasible technologies may be developed to enhance the health functionality of small fruit crops.     

Phosphatase activity in earthworm faeces

Wormcasts of Allolobophora caliginosa have been shown to have higher phosphatase activity than occurs in uningested soil, resulting in an increase in inorganic P released by mineralization of organic P. This paper describes similar observations on organic wastes which may be used for vermiculture. Besides A. caliginosa, three species which will feed on dung or other organic substrates were investigated, Eisenia foetida, Dendrobaena veneta and Lumbricus rubellus. When cow dung was used as a substrate, background phosphatase activity was too high for the effects of earthworm activity to be detected and a culture medium was therefore developed from sterilized paper waste sludge with added phytin. Phosphatase activity, assayed by a modified Hoffman method, was higher in the presence of all four earthworm species than in controls. It showed two peaks in relation to pH, at 3–5 and 9–10. The former is attributed to microbial activity and the latter to microbial activity or earthworm alkaline phosphatase. After 1 month, cultures of paper waste sludge with phytin contained about twice as much water soluble P when worms were present than in their absence.     

Degradation of lignin in wheat straw during growth of the oyster mushroom (Pleurotus ostreatus) using off-line thermochemolysis with tetramethylammonium hydroxide and solid-state (13)C NMR.

The oyster mushroom (Pleurotus ostreatus) is widely cultivated on wheat straw (Triticum aestivum); however, there is a need to better understand the relationship between the chemical composition of the compost and mushroom growth. Wheat straw was degraded over a period of 63 days by P. ostreatus during which time it was sampled at weekly intervals. Off-line thermochemolysis with tetramethylammonium hydroxide and solid-state (13)C NMR were then used in the molecular characterization of the undegraded wheat straw and the degraded samples. The degraded wheat straw samples had a lower proportion of syringyl- to guaiacyl-derived moieties and cinnamyl- to guaiacyl-derived moieties than the undegraded control. There were increases in both guaiacyl and syringyl acid to aldehyde ratios with composting time, which showed that side-chain oxidation has been mediated by P. ostreatus. The (13)C NMR spectra confirmed the increase in carboxyl content but indicated that the overall lignin and methoxyl contents remained relatively constant, although some nonsystematic variations were observed. The spectra also showed a decrease in amorphous noncellulosic polysaccharides in relation to the crystalline cellulose upon degradation.     

Factors affecting the caffeine and polyphenol contents of black and green tea infusions.

The effects of product and preparation variables on the in-cup chemical composition of tea extracts is of interest because the appearance and taste characteristics and the possible health effects of a tea liquor arise from the chemical components extracted from the leaf during tea preparation. A comprehensive study was therefore undertaken to determine the contributions of product and preparation variables on the total soluble solids, caffeine, and polyphenol contents of tea extracts. The results of this study show that the variety, growing environment, manufacturing conditions, and grade (particle size) of the tea leaves each influence the tea leaf and final infusion compositions. In addition, the composition of the tea infusion was shown to be influenced by whether the tea was contained in a teabag and, if so, the size and material of construction of the bag. Finally, the preparation method, including the amounts of tea and water used, infusion time, and amount of agitation, was shown to be a major determinant of the component concentrations of tea beverages as consumed. An illustration of the variation introduced by these product and preparation factors is provided by comparing solids, caffeine, and polyphenol contents of green and black tea infusions when commercial products are prepared according to the instructions given on their packaging.     

Effects of Different Factors on Concentration of Functional Components of Aronia and Saskatoon Berries

Plant Foods for Human Nutrition - Effects of different factors on the content of phenolics, anthocyanins, antioxidants and colour parameters in two varieties of Aronia and three varieties of...     

Forms of memory failure

Memory may fail in a variety of ways. Patients with Korsakoff's syndrome demonstrate global memory deficits similar to those seen in patients with early progressive dementia. Korsakoff's patients, however, may recall rules and principles for organizing information and can gain access to their previously acquired knowledge (semantic memory), whereas recent memory may be grossly impaired. In contrast, dementia patients may have little access to previously acquired knowledge and therefore have great difficulty in organizing and encoding ongoing events. These contrasting forms of memory failure have implications for understanding the structure and mechanisms of memory and learning, particularly the relationship between episodic and semantic memory, as well as the development of therapeutic strategies for cognitive impairments.     

Extinction and ecosystem function in the marine benthos

Rapid changes in biodiversity are occurring globally, yet the ecological impacts of diversity loss are poorly understood. Here we use data from marine invertebrate communities to parameterize models that predict how extinctions will affect sediment bioturbation, a process vital to the persistence of aquatic communities. We show that species extinction is generally expected to reduce bioturbation, but the magnitude of reduction depends on how the functional traits of individual species covary with their risk of extinction. As a result, the particular cause of extinction and the order in which species are lost ultimately govern the ecosystem-level consequences of biodiversity loss.