Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Leaf N, P and N:P ratios and measurements of environmental factors in an temperate steppe, Xilin River Basin, Inner Mongolia, China

Include leaf N, P and N:P ratios of 80 species in 1979 and 2006, soil traits of the sampling sites, the comparison of the two leaf N determination methods (Kjeldahl N determination and elemental analyzer), the precipitation of Xilin River Basin from 1953 to 2011

The first complete mitochondrial genome of eggplant (Solanum melongena)

Eggplant is an important vegetable crop because of its rich nutrition, but to date no mitochondrial genome has been reported. In this study, the complete mitochondrial genome of the eggplant was sequenced. The complete mitochondrial genome was 498,136bp, linear structure, containing 54 protein-coding genes, four rRNAs, and 32 tRNAs. The phylogenetic tree supported the hypothesis that the eggplant is most closely related to Solanum tuberosum and Solanum lycopersicum

Data from: Leaf P increase outpaces leaf N in an Inner Mongolia grassland over 27 years

The dynamics of leaf nitrogen (N) and phosphorus (P) have been intensively explored in short-term experiments, but rarely at longer timescales. Here, we investigated leaf N : P stoichiometry over a 27-year interval in an Inner Mongolia grassland by comparing leaf N : P concentration of 2006 with that of 1979. Across 80 species, both leaf N and P increased, but the increase in leaf N lagged behind that of leaf P, leading to a significant decrease in the N : P ratio. These changes in leaf N : P stoichiometry varied among functional groups. For leaf N, grasses increased, woody species tended to increase, whereas forbs showed no change. Unlike leaf N, leaf P of grasses and forbs increased, whereas woody species showed no change. Such changes may reflect N deposition and P release induced by soil acidification over the past decades. The interannual effect of precipitation may somewhat have reduced the soil available N, leading to the more modest increase of leaf N than of leaf P. Thus, leaf N : P stoichiometry significantly responded to long-term environmental changes in this temperate steppe, but different functional groups responded differently. Our results indicate that conclusions of plant stoichiometry under short-term N fertilization should be treated with caution when extrapolating to longer timescales

Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids

The chloroplast genomic information was obtained from three wild Solanum and four hybrids by chloroplast genome sequencing. The chloroplast genomes of the seven samples comprise of a circular structure and sizes from 155,581 to 155,612 bp and composed of 130 genes. The genome structures of the two hybrids were identical, while the other two hybrids showed 2 bp differences in the LSC when compared with their maternal parent. The total sites of SNP and InDel were 39–344 and 54–90, respectively. With the exception of one hybrid with two additional sites, the other hybrids were identical to their maternal

Unraveling new roles for serotonin receptor 2B in development: key findings from Xenopus

The serotonin receptor 5-HT2B has been shown to be critically important during embryogenesis as the knockout of this gene in mice causes heart defects and embryonic lethality that impairs further analyses on other embryonic cell and tissue types. In the present review we highlight how the use of Xenopus laevis, an alternative vertebrate model suitable for gene loss and gain of function analyses, contributed to our understanding of the role of 5-HT2B signaling during development. In vivo studies showed that the 5-HT2B signaling is not only required for heart development but also has a crucial role in ocular and craniofacial morphogenesis being involved in shaping the first branchial arch and the jaw joint, in the retinogenesis and possibly in the periocular mesenchyme development. These findings may be relevant for our understanding of congenital defects including human birth malformations. In addition, the 5-HT2B appears to be required for the therapeutic actions of selective serotonin reuptake inhibitors commonly prescribed as antidepressant drugs to pregnant and lactating women. We discuss how the understanding of the molecular basis of the serotonin signaling in a suitable animal model embryogenesis may open new lines of investigations and therapies in humans

Additional file 1: Figure S1. of ULK1 phosphorylates Sec23A and mediates autophagy-induced inhibition of ER-to-Golgi traffic

Aggregation of ERES fluorescence puncta during active autophagy. Boxed areas of the pericentriolar ERES from cells grown in growth medium (left) and amino acid starved medium (right) were plotted as a function of the XY position of each pixel from the boxed area. The number of signal peaks was reduced in amino acid starved medium but the size of the peaks was larger, indicating aggregation of ERES signals into fewer and brighter fluorescence puncta. (TIFF 4537 kb

Additional file 6: Figure S6. of ULK1 phosphorylates Sec23A and mediates autophagy-induced inhibition of ER-to-Golgi traffic

The interactions between the ULK1 phosphorylation mutants of Sec23A and Sec31A. (A) S207 and T405 mutants of Sec23A were tested for their interaction with Sec31A by co-expressing the Myc-His-Sec23A mutants and GFP-Sec31A. (B) Combinations of S207 and T405 double mutants were tested for the interaction with Sec31A. Overexpression of the indicated protein was carried in HEK293T cells, followed by immunoprecipitation of Myc-His-Sec23A by anti-Myc antibody. Co-precipitated GFP-Sec31A was detected by anti-GFP antibody. (B) Wildtype Sec23A, S207A and T405A mutants were tested for the interaction with GFP-Sec31A in growth medium or in amino acid starved medium EBSS. (TIFF 5305 kb

Comparative transcriptome analysis provides insights into the molecular mechanism underlying double fertilization between self-crossed Solanum melongena and that hybridized with Solanum aethiopicum.

Wild relatives represent a source of variation for many traits of interest for eggplant (Solanum melongena) breeding, as well as for broadening its genetic base. However, interspecific hybridization with wild relatives has been barely used in eggplant breeding programs, and reproductive barriers have resulted in reduced seed numbers in interspecific combinations. The mechanism underlying this phenomenon remains unclear. We hybridized females of cultivated eggplant 177 (Solanum melongena) with males of wild relatives 53 and Y11 (Solanum aethiopicum). Self-crossed 177 was the control. The seed number per control fruit was significantly higher than that of the hybrids. Paraffin sections showed no significant difference between control and 177×53 and 177×Y11. Double fertilization began 4 days post-pollination. Sperm cells were fused with egg cells 6 days post-pollination. To understand the differences in molecular mechanisms underlying this process, transcriptomes of ovaries at 0, 4, and 6 days after self-crossing and hybridization were analyzed. We screened 22,311 differentially expressed genes (DEGs) between the control and hybrids 4 and 6 days post-pollination. A total of 497 DEGs were shared among all pollination combinations. These DEGs were enriched in plant hormone transduction, cell senescence, metabolism, and biosynthesis pathways. DEG clustering analysis indicated distinct expression patterns between the control and hybrids but not between the hybrids. The DEGs in hybrids involved secondary metabolic process, phenylpropanoid metabolic process, and carboxypeptidase activity, while those in the control involved xyloglucan metabolic process, auxin-activated signaling pathway, cell wall polysaccharide metabolic process, and xyloglucosyl transferase activity. Additionally, 1683 transcription factors, including members of the AP2-ERF, MYB, bHLH, and B3 families may play important roles in self-crossing and hybridization. Our results provide insights into the regulatory mechanisms underlying variations between ovaries of self-crossed and hybrid eggplants and a basis for future studies on crossbreeding Solanum and genetic mechanisms underlying double fertilization