Water limitation effect on seed development and germination in Trigonella coerulea (Fabaceae)

The annual garden spice legume Trigonella coerulea was subjected to controlled drought conditions to investigate the influence of resource limitation on flowering, seed production and germination. Limitations in water availability significantly reduced plant height and the number of fruits produced. However, treatments had no significant effect on seed set within the fruit. Fruit number per plant, rather than seed number per fruit was affected by resource limitation. Plants growing under water deficiency had higher flower abortion rates. Simultaneously, the size and germination rate of the seeds were decreased. In terms of reproductive success T. coerulea was not able to adapt reproduction to water shortage. Increase in moisture had no significant effect on seed quantity and quality when compared to the control.     

Population fragmentation may reduce fertility to zero in Banksia goodii — a demonstration of the Allee effect

All individuals of all known populations of Banksia goodii were assessed for seed production. Small populations produced no or only a few seeds per unit canopy area. Effects of population size on seed production per unit area and seed production per plant were present over the whole range of population sizes, indicating that even in large populations seed production may still not be at its maximum. Resource differences could not explain this disproportionate decrease in seed production with decline in population size, because there were no differences in soil properties and understorey or overstorey cover between the small and large populations. Although plants in small and large populations were similar in size, seed production per plant was much lower in small populations. This was not because plants in small populations produced fewer cones but because the fraction of these cones that was fertile was much lower. Five of the nine smallest populations (<200 m²) produced no fertile cones over the last 10 years. The number of seeds per fertile cone did not depend on population size. The results are discussed in relation to pollination biology.     

Identification of novel prognostic alternative splicing signature in papillary renal cell carcinoma

Papillary renal cell carcinoma (pRCC) is a heterogeneous disease containing multifocal or solitary tumors with an aggressive phenotype. Increasing evidence has indicated the involvement of aberrant splicing variants in renal cell cancer, while systematic profiling of aberrant alternative splicing (AS) in pRCC was lacking and largely unknown. In the current study, comprehensive profiling of AS events were performed based on the integration of pRCC cohort from the Cancer Genome Atlas database and SpliceSeq software. With rigorous screening and univariate Cox analysis, a total of 2077 prognoses AS events from 1642 parent genes were identified. Then, stepwise least absolute shrinkage and selection operator method-penalized Cox regression analyses with 10-fold cross-validation followed by multivariate Cox regression were used to construct the prognostic AS signatures within each AS type. And a final 21 AS event-based signature was proposed which showed potent prognostic capability in stratifying patients into low- and high-risk subgroups (P < .0001). Furthermore, time-dependent receiver operating characteristics curves confirmed that the final AS signature was effective and robust in predicting overall survival for pRCC patients with the area under the curve above 0.9 from 1 to 5 years. In addition, splicing correlation network was built to uncover the potential regulatory pattern among prognostic splicing factors and candidate AS events. Besides, gene set enrichment analysis revealed the involvement of these candidates AS events in tumor-related pathways including extracellular matrix organization, oxidative phosphorylation, and P53 signaling pathways. Taken together, our results could contribute to elucidating the underlying mechanism of AS in the oncogenesis process and broaden the novel field of prognostic and clinical application of molecule-targeted approaches in pRCC.     

Effects of season and population size on pollination and reproductive output in a Mediterranean shrub

• Pollinator guilds may change throughout extended flowering periods, affecting plant reproductive output, especially in seasonal climates. We hypothesised a seasonal shift in pollinator guild and an autumn reduction in pollinator abundance, especially in small and sparse populations.
• We recorded pollinator identity, abundance and behaviour in relation to flower density from plant to population throughout the extended flowering of Ononis tridentata. We evaluated female reproductive output by recording pollination success and pre‐dispersal seed predation in eight populations of contrasting size and density. Offspring quality was also characterised through seed weight and germination.
• A diverse guild of insects visited O. tridentata in spring, while only Apis mellifera was observed in autumn. Visitation frequency did not vary seasonally, but the number of flowers per foraging bout was lower, and seeds were heavier and had a higher germination rate in autumn. Plant and neighbourhood flowering display were not related to pollinator visitation frequency or behaviour. However, the rate of fertilised ovules, seed set and autumn flowering display size were positively related to population density.
• The maintenance of pollination in autumn enhances the reproductive performance of O. tridentata due to higher quality of autumn seed, and to a large reduction in seed predator pressure. We also suggest that observed changes in pollinator behaviour could be one of the processes behind seasonal variation in seed performance, since geitonogamous crosses were less likely to occur in autumn.

     

Floral display size in comfrey, Symphytum officinale L. (Boraginaceae): relationships with visitation by three bumblebee species and subsequent seed set

The fecundity of insect-pollinated plants may not be linearly related to the number of flowers produced, since floral display will influence pollinator foraging patterns. We may expect more visits to plants with more flowers, but do these large plants receive more or fewer visits per flower than small plants? Do all pollinator species respond in the same way? We would also expect foragers to move less between plants when the number of flowers per plant are large, which may reduce cross-pollination compared to plants with few flowers. We examine the relationships between numbers of inflorescence per plant, bumblebee foraging behaviour and seed set in comfrey, Symphytum officinale, a self-incompatible perennial herb. Bumblebee species differed in their response to the size of floral display. More individuals of Bombus pratorum and the nectar-robbing B.?terrestris were attracted to plants with larger floral displays, but B. pascuorum exhibited no increase in recruitment according to display size. Once attracted, all bee species visited more inflorescences per plant on plants with more inflorescences. Overall the visitation rate per inflorescence and seed set per flower was independent of the number of inflorescences per plant. Variation in seed set was not explained by the numbers of bumblebees attracted or by the number of inflorescences they visited for any bee species. However, the mean seed set per flower (1.18) was far below the maximum possible (4 per flower). We suggest that in this system seed set is not limited by pollination but by other factors, possibly nutritional resources.     

Ranked set sampling for replicated sampling designs

In practical ecological sampling studies, a certain design (such as plot sampling or line-intercept sampling) is usually replicated more than once. For each replication, the Horvitz-Thompson estimation of the objective parameter is considered. Finally, an overall estimator is achieved by averaging the single Horvitz-Thompson estimators. Because the design replications are drawn independently and under the same conditions, the overall estimator is simply the sample mean of the Horvitz-Thompson estimators under simple random sampling. This procedure may be wisely improved by using ranked set sampling. Hence, we propose the replicated protocol under ranked set sampling, which gives rise to a more accurate estimation than the replicated protocol under simple random sampling.     

Fruit set in a deceptive orchid: The effect of flowering phenology,display size,and local floral abundance

We investigated the effect of flowering time, display size, and local floral density on fruit set in Tolumnia variegata, a pollination-limited orchid that offers no reward to its pollinator(s). During 1990, natural variation in flowering time, display size, and fruit set were monitored in 508 plants at one locality in Puerto Rico. The following season, orchid floral abundance per host tree (Randia aculeata) was manipulated to investigate its effect on fruit set. Four floral abundance treatments were established (700, 500, 300, and 100), each replicated four times. Flowering time was the most important trait affecting fruit set. The proportion of plants setting at least one fruit was significantly high early and late in the season, but low during the flowering peak. Thus, strong disruptive selection differential on flowering phenology was found. Display size had little effect on fruit set. A weak, but significant disruptive selection differential on display size was found. Orchid floral abundance per host tree had a significant effect on fruit set. Early in the season, T. variegata flowers with intermediate number of conspecific flowers exhibited a greater probability of setting fruit than those in host trees with fewer or more flowers. Our results show that flowering phenology may be evolutionarily unstable, possibly a consequence of the deception pollination system. Furthermore, a deception strategy would be relatively unsuccessful in populations where plants are found in either very dense or sparse patches.     

The Multivariate Nonparametric Methods for Identifying Gene Sets with Differential Expression

Background

Gene Set Analysis (GSA) identifies differential expression gene sets amid the different phenotypes. The results of published papers in this filed are inconsistent and there is no consensus on the best method. In this paper two new methods, in comparison to the previous ones, are introduced for GSA.

Methods

The MMGSA and MRGSA methods based on multivariate nonparametric techniques were presented. The implementation of five GSA methods (Hotelling's T², Globaltest, Abs_Cat, Med_Cat and Rs_Cat) and the novel methods to detect differential gene expression between phenotypes were compared using simulated and real microarray data sets.

Results

In a real dataset, the results showed that the powers of MMGSA and MRGSA were as well as Globaltest and Tsai. The MRGSA method has not a good performance in the simulation dataset.

Conclusions

The Globaltest method is the best method in the real or simulation datasets. The performance of MMGSA in simulation dataset is good in small-size gene sets. The GLS methods are not good in the simulated data, except the Med_Cat method in large-size gene sets.