Increasing the Efficiency of Microsatellite Discovery from Poorly Enriched Libraries in Coniferous Forest Species

Microsatellites are PCR based markers widely applicable in many plant species. Although the discovery and development of new microsatellites is a costly and technically demanding process, they are widely used in many plant systems. In coniferous tree species, the large genome size and repetitive DNA regions further aggravate the process, often resulting in libraries with very low enrichment efficiencies. Such species have proven intractable to efficient microsatellite discovery. For example, enriched microsatellite libraries produced for seven angiosperm species had enrichment efficiencies up to 50%, whereas libraries for three conifers, generated concurrently, under identical conditions, all had enrichment efficiencies below 10%. This report describes a simple strategy for recovering useful microsatellites from two of these conifer libraries, Pinus elliottii and Araucaria cuninghamii. Enrichment efficiencies increased from 0% to 100% and 1.5% to 98%, respectively. The strategy utilised DIG labelled oligo probes to identify clones containing microsatellite inserts. The technique is cost effective and rapid, utilising basic techniques and equipment that are widely available.     

Nitrogen and phosphorus addition differentially enhance seed production of dominant species in a temperate steppe

Previous studies have demonstrated changes in plant growth and reproduction in response to nutrient availability, but responses of plant growth and reproduction to multiple levels of nutrient enrichment remain unclear. In this study, a factorial field experiment was performed with manipulation of nitrogen (N) and phosphorus (P) availability to examine seed production of the dominant species, Stipa krylovii, in response to N and P addition in a temperate steppe. There were three levels of N and P addition in this experiment, including no N addition (0 g N m⁻² year⁻¹), low N addition (10 g N m⁻² year⁻¹), and high N addition (40 g N m⁻² year⁻¹) for N addition treatment, and no P addition (0 g P m⁻² year⁻¹), low P addition (5 g P m⁻² year⁻¹), and high P addition (10 g P m⁻² year⁻¹) for P addition treatment. Low N addition enhanced seed production by 814%, 1371%, and 1321% under ambient, low, and high P addition levels, respectively. High N addition increased seed production by 2136%, 3560%, and 3550% under ambient, low, and high P addition levels, respectively. However, P addition did not affect seed production in the absence of N addition, but enhanced it under N addition. N addition enhanced seed production mainly by increasing the tiller number and inflorescence abundance per plant, whereas P addition stimulated it by decreasing the plant density yet stimulating height of plants and their seed number per inflorescence. Our results indicate seed production is not limited by P availability but rather by N availability in the temperate steppe, whereas seed production will be increased by P addition when N availability is improved. These findings enable a better understanding of plant reproduction dynamics in the temperate steppe under intensified nutrient enrichment and can inform their improved management in the future.     

Combining Global and Marginal Tests to Compare Two Treatments on Multiple Endpoints

We consider the problem of comparing two treatments on multiple endpoints where the goal is to identify the endpoints that have treatment effects, while controlling the familywise error rate. Two current approaches for this are (i) applying a global test within a closed testing procedure, and (ii) adjusting individual endpoint p‐values for multiplicity. We propose combining the two current methods. We compare the combined method with several competing methods in a simulation study. It is concluded that the combined approach maintains higher power under a variety of treatment effect configurations than the other methods and is thus more power‐robust.     

On the False Discovery Rate and Expected Type I Errors

The paper is concerned with expected type I errors of some stepwise multiple test procedures based on independent p‐values controlling the so‐called false discovery rate (FDR). We derive an asymptotic result for the supremum of the expected type I error rate(EER) when the number of hypotheses tends to infinity. Among others, it will be shown that when the original Benjamini‐Hochberg step‐up procedure controls the FDR at level α, its EER may approach a value being slightly larger than α/4 when the number of hypotheses increases. Moreover, we derive some least favourable parameter configuration results, some bounds for the FDR and the EER as well as easily computable formulae for the familywise error rate (FWER) of two FDR‐controlling procedures. Finally, we discuss some undesirable properties of the FDR concept, especially the problem of cheating.     

A Bootstrap Procedure for Adaptive Selection of the Test Statistic in Flexible Two‐Stage Designs

Adaptive two‐stage designs allow a data‐driven change of design characteristics during the ongoing trial. One of the available options is an adaptive choice of the test statistic for the second stage of the trial based on the results of the interim analysis. Since there is often only a vague knowledge of the distribution shape of the primary endpoint in the planning phase of a study, a change of the test statistic may then be considered if the data indicate that the assumptions underlying the initial choice of the test are not correct. Collings and Hamilton proposed a bootstrap method for the estimation of the power of the two‐sample Wilcoxon test for shift alternatives. We use this approach for the selection of the test statistic. By means of a simulation study, we show that the gain in terms of power may be considerable when the initial assumption about the underlying distribution was wrong, whereas the loss is relatively small when in the first instance the optimal test statistic was chosen. The results also hold true for comparison with a one‐stage design. Application of the method is illustrated by a clinical trial example.     

Effects of social and inanimate enrichment on the behavior of yearling rhesus monkeys

Certain types of inanimate environmental enrichment have been shown to positively affect the behavior of laboratory primates, as has housing them in appropriate social conditions. While social housing is generally advocated as an important environmental enhancement, few studies have attempted to measure the influence of social conditions on the effects of inanimate enrichment or to compare the relative merits of social and inanimate enhancements. In the present study, inanimate enrichment (predominately physical and feeding enhancements) resulted in increased species-typical behavior for socially restricted subjects. However, social enrichment (living in groups) appeared to be more beneficial for young rhesus monkeys, leading to increased species-typical activities and decreased abnormal activities. The behavior of one cohort of yearling rhesus monkeys (Macaca mulatta) housed in small peer groups was compared with the behavior of four yearling cohorts housed in single cages. Half the animals in each cohort received a three-phase enrichment program and the rest served as controls. Group-housed yearlings spent significantly more time feeding and exploring and significantly less time behaving abnormally, self-grooming, and drinking than did singly housed yearlings. Enriched subjects spent significantly more time playing by themselves, and significantly less time self-grooming and exploring than did controls. Among group-housed subjects only, there were no differences between enriched and control monkeys. Captive primates should be housed socially, whenever appropriate, as the first and most important step in an enrichment program, with the provision of inanimate enhancements being considerably less important. Limited resources for inanimate enrichment programs instead should be focused on those individuals who can not be housed socially. © 1996 Wiley-Liss, Inc.     

沙枣果总黄酮类化合物的富集研究

通过对9种型号大孔吸附树脂静态筛选,最终确定AB-8型大孔吸附树脂用于沙枣果总黄酮化合物的富集,并通过动态实验,确定沙枣果总黄酮最优富集条件为：样品浓度2.43 mg·mL^-1,上样速率2 BV·h^-1,乙醇浓度70%,洗脱速率2 BV·h^-1。在最优工艺条件下,沙枣果总黄酮浓度由9.73%增加到49.52%;其中金丝桃苷含量由0.53%增加到3.07%,提高5.79倍。本研究为沙枣果总黄酮的开发利用提供了理论依据。     

Fast further purification of diastereomeric salts of a nonracemic acid by gas antisolvent fractionation

A novel, green possibility of the further purification of the diastereomeric salt of 4‐chloromandelic acid and 1‐phenylethane‐1‐amine was developed. Gas antisolvent method using supercritical carbon dioxide was applied for the first time to precipitate the diastereomeric salts with increased purity followed by the supercritical fluid extraction of the dissolved diastereomers. The RR ‐salt can be purified to >99%, while fractionation‐based purification of the SR ‐salt is limited to ~80%. The limiting initial diastereomeric excess correlates strongly with the atmospheric melting eutectic composition of the same salts, which suggests that despite the fast precipitation, the diastereomeric excess of the solid product is not kinetically determined. The efficiency of the diastereomeric enrichment is in the same range as that of the atmospheric reference experiments; however, technological advantages provided by the antisolvent precipitation method such as fast processing and dry product obtained suggest that this novel procedure is a promising alternative to the atmospheric methods.     

The roles of motor activity and environmental enrichment in intellectual disability

In people with intellectual disabilities, an enriched environment can stimulate the acquisition of motor skills and could partially repair neuronal impairment thanks to exploration and motor activity. A deficit in environmental and motor stimulation leads to low scores in intelligence tests and can cause serious motor skill problems. Although studies in humans do not give much evidence for explaining basic mechanisms of intellectual disability and for highlighting improvements due to enriched environmental stimulation, animal models have been valuable in the investigation of these conditions. Here, we discuss the role of environmental enrichment in four intellectual disabilities: Foetal Alcohol Spectrum Disorder (FASD), Down, Rett, and Fragile X syndromes.     

Combining affinity enrichment,cross‐linking with photo amino acids,and mass spectrometry for probing protein kinase D2 interactions

We present a novel approach that relies on the affinity capture of protein interaction partners from a complex mixture, followed by their covalent fixation via UV‐induced activation of incorporated diazirine photoreactive amino acids (photo‐methionine and photo‐leucine). The captured protein complexes are enzymatically digested and interacting proteins are identified and quantified by label‐free LC/MS analysis. Using HeLa cell lysates with photo‐methionine and photo‐leucine‐labeled proteins, we were able to capture and preserve protein interactions that are otherwise elusive in conventional pull‐down experiments. Our approach is exemplified for mapping the protein interaction network of protein kinase D2, but has the potential to be applied to any protein system. Data are available via ProteomeXchange with identifiers PXD005346 (photo amino acid incorporation) and PXD005349 (enrichment experiments).