Revisiting ancestral polyploidy in plants

Whole-genome duplications (WGDs) or polyploidy events have been studied extensively in plants. In a now widely cited paper, Jiao et al. presented evidence for two ancient, ancestral plant WGDs predating the origin of flowering and seed plants, respectively. This finding was based primarily on a bimodal age distribution of gene duplication events obtained from molecular dating of almost 800 phylogenetic gene trees. We reanalyzed the phylogenomic data of Jiao et al. and found that the strong bimodality of the age distribution may be the result of technical and methodological issues and may hence not be a "true" signal of two WGD events. By using a state-of-the-art molecular dating algorithm, we demonstrate that the reported bimodal age distribution is not robust and should be interpreted with caution. Thus, there exists little evidence for two ancient WGDs in plants from phylogenomic dating

Early spring subglacial discharge plumes fuel under-ice primary production at a Svalbard tidewater glacier

Subglacial upwelling of nutrient-rich bottom water is known to sustain elevated summer primary production in tidewater-glacier-influenced fjord systems. However, the importance of subglacial upwelling during the early spring season has not been considered yet. We hypothesized that subglacial discharge under sea ice is present in early spring and that its flux is sufficient to increase phytoplankton primary productivity. We evaluated the effects of the submarine discharge on primary production in a seasonally fast-ice covered Svalbard fjord (Billefjorden) influenced by a tidewater outlet glacier in April and May 2019. We found clear evidence for subglacial discharge and upwelling. Although the estimated bottom-water entrainment factor (1.6) and total fluxes were lower than in summer studies, we still observed substantial impact on the fjord ecosystem and primary production at this time of the year. The subglacial discharge leads to a salinity-stratified surface water layer and sea ice formation with low bulk salinity and permeability. The combination of the stratified surface layer, a 2-fold higher under-ice irradiance due to thinner snow cover, and higher N and Si concentrations at the glacier front supported phytoplankton primary production 2 orders of magnitude higher (42.6 mg C m−2 d−1) compared to a marine reference site at the fast-ice edge. Reciprocal transplant experiments showed that nutrient supply increased phytoplankton primary production by approximately 30 %. The brackish-water sea ice at the glacier front with its low bulk salinity contained a reduced brine volume, limiting the inhabitable brine channel space and nutrient exchange with the underlying seawater compared to full marine sea ice. Microbial and algal communities were substantially different in subglacial-influenced water and sea ice compared to the marine reference site, sharing taxa with the subglacial outflow water. We suggest that with climate change, the retreat of tidewater glaciers in early spring could lead to decreased under-ice phytoplankton primary production. In contrast, sea ice algae production and biomass may become increasingly important, unless sea ice disappears first, in which case spring phytoplankton primary production may increase

HER2 and p95HER2 differentially regulate miRNA expression in MCF-7 breast cancer cells and downregulate MYB proteins through miR-221/222 and miR-503

Mecanismes de la malaltia; Càncer de mamaMecanismos de la enfermedad; Cáncer de mamaDisease Mechanisms; Breast CancerThe HER2 oncogene and its truncated form p95HER2 play central roles in breast cancer. Here, we show that although HER2 and p95HER2 generally elicit qualitatively similar changes in miRNA profile in MCF-7 breast cancer cells, a subset of changes are distinct and p95HER2 shifts the miRNA profile towards the basal breast cancer subtype. High-throughput miRNA profiling was carried out 15, 36 and 60 h after HER2 or p95HER2 expression and central hits validated by RT-qPCR. miRNAs strongly regulated by p95HER2 yet not by HER2, included miR-221, miR-222, miR-503, miR-29a, miR-149, miR-196 and miR-361. Estrogen receptor-α (ESR1) expression was essentially ablated by p95HER2 expression, in a manner recapitulated by miR-221/-222 mimics. c-Myb family transcription factors MYB and MYBL1, but not MYBL2, were downregulated by p95HER2 and by miR-503 or miR-221/-222 mimics. MYBL1 3′UTR inhibition by miR-221/222 was lost by deletion of a single putative miR-221/222 binding sites. p95HER2 expression, or knockdown of either MYB protein, elicited upregulation of tissue inhibitor of matrix metalloprotease-2 (TIMP2). miR-221/222 and -503 mimics increased, and TIMP2 knockdown decreased, cell migration and invasion. A similar pathway was operational in T47D- and SKBr-3 cells. This work reveals important differences between HER2- and p95HER2- mediated miRNA changes in breast cancer cells, provides novel mechanistic insight into regulation of MYB family transcription factors by p95HER2, and points to a role for a miR-221/222– MYB family–TIMP2 axis in regulation of motility in breast cancer cells.This work was supported by the Danish Council for Independent Research (grants no. 12-126942 and 12-127290 to SFP), by the Hartmann foundation (SFP), Fondation Juchum (SFP), Kirsten og Freddy Johansens Fond (SFP), the Breast Cancer Research Foundation (BCRF-17-008) (JA), Instituto de Salud Carlos III (PI16/00253) (JA) and the Harboe foundation (SFP). Katrine Franklin Mark is gratefully acknowledged for excellent technical assistance. We are grateful to Pascal Pineau from Institut Pasteur, France for the MYBL1 3′UTR/psiCHECK2 construct

<i>HER2</i>-encoded mir-4728 forms a receptor-independent circuit with miR-21-5p through the non-canonical poly(A) polymerase PAPD5

We previously reported that the human HER2 gene encodes the intronic microRNA mir-4728, which is overexpressed together with its oncogenic host gene and may act independently of the HER2 receptor. More recently, we also reported that the oncogenic miR-21-5p is regulated by 3′ tailing and trimming by the non-canonical poly(A) polymerase PAPD5 and the ribonuclease PARN. Here we demonstrate a dual function for the HER2 locus in upregulation of miR-21-5p; while HER2 signalling activates transcription of mir-21, miR-4728-3p specifically stabilises miR-21-5p through inhibition of PAPD5. Our results establish a new and unexpected oncogenic role for the HER2 locus that is not currently being targeted by any anti-HER2 therapy

The Araucaria Project. First Cepheid Distance to the Sculptor Group Galaxy NGC 7793 from Variables discovered in a Wide-Field Imaging Survey

We have detected, for the first time, Cepheid variables in the Sculptor Group spiral galaxy NGC 7793. From wide-field images obtained in the optical V and I bands on 56 nights in 2003-2005, we have discovered 17 long-period (24-62 days) Cepheids whose periods and mean magnitudes define tight period-luminosity relations. We use the (V-I) Wesenheit index to determine a reddening-free true distance modulus to NGC 7793 of 27.68 +- 0.05 mag (internal error) +- 0.08 mag (systematic error). The comparison of the reddened distance moduli in V and I with the one derived from the Wesenheit magnitude indicates that the Cepheids in NGC 7793 are affected by an average total reddening of E(B-V)=0.08 mag, 0.06 of which is produced inside the host galaxy. As in the earlier Cepheid studies of the Araucaria Project, the reported distance is tied to an assumed LMC distance modulus of 18.50. The quoted systematic uncertainty takes into account effects like blending and possible inhomogeneous filling of the Cepheid instability strip on the derived distance. The reported distance value does not depend on the (unknown) metallicity of the Cepheids according to recent theoretical and empirical results. Our Cepheid distance is shorter, but within the errors consistent with the distance to NGC 7793 determined earlier with the TRGB and Tully-Fisher methods. The NGC 7793 distance of 3.4 Mpc is almost identical to the one our project had found from Cepheid variables for NGC 247, another spiral member of the Sculptor Group located close to NGC 7793 on the sky. Two other conspicuous spiral galaxies in the Sculptor Group, NGC 55 and NGC 300, are much nearer (1.9 Mpc), confirming the picture of a very elongated structure of the Sculptor Group in the line of sight put forward by Jerjen et al. and others.Comment: AJ in pres

The Araucaria Project. Determination of the LMC Distance from Late-Type Eclipsing Binary Systems: I. OGLE-051019.64-685812.3

We have analyzed the double-lined eclipsing binary system OGLE-051019.64-685812.3 in the LMC which consists of two G4 giant components with very similar effective temperatures. A detailed analysis of the OGLE I-band light curve of the system, radial velocity curves for both components derived from high-resolution spectra, and near-infrared magnitudes of the binary system measured outside the eclipses has allowed us to obtain an accurate orbit solution for this eclipsing binary, and its fundamental physical parameters. Using a surface brightness-(V-K) color relation for giant stars we have calculated the distance to the system and obtain a true distance modulus of 18.50 mag, with an estimated total uncertainty of ~ 3 %. More similar eclipsing binary systems in the LMC which we have discovered and for which we are currently obtaining the relevant data will allow us to better check on the systematics of the method and eventually provide a distance determination to the LMC accurate to 1 percent, so much needed for the calibration of the distance scale.Comment: ApJ accepte