The HARPS search for southern extra-solar planets

The meter-per-second precision achieved by today’s velocimeters enables us to search for 1−10 M⊕ planets in the habitable zone of cool stars. This paper reports on the detection of three planets orbiting GJ 163 (HIP 19394), a M3 dwarf monitored by our ESO/HARPS search for planets. We made use of the HARPS spectrograph to collect 150 radial velocities of GJ 163 over a period of eight years. We searched the radial-velocity time series for coherent signals and found five distinct periodic variabilities. We investigated the stellar activity and called into question the planetary interpretation for two signals. Before more data can be acquired we concluded that at least three planets are orbiting GJ 163. They have orbital periods of Pb = 8.632 ± 0.002, Pc = 25.63 ± 0.03, and Pd = 604 ± 8 days and minimum masses msini = 10.6 ± 0.6, 6.8 ± 0.9, and 29 ± 3 M⊕, respectively. We hold our interpretations for the two additional signals with periods P(e) = 19.4 and P(f) = 108 days. The inner pair presents an orbital period ratio of 2.97, but a dynamical analysis of the system shows that it lays outside the 3:1 mean motion resonance. The planet GJ 163c, in particular, is a super-Earth with an equilibrium temperature of Teq = (302 ± 10)(1 − A)1/4 K and may lie in the so-called habitable zone for albedo values (A = 0.34 − 0.89) moderately higher than that of Earth (A⊕ = 0.2−0.3).

The HARPS search for southern extra-solar planets

The vast diversity of planetary systems detected to date is defying our capability of understanding their formation and evolution. Well-defined volume-limited surveys are the best tool at our disposal to tackle the problem, via the acquisition of robust statistics of the orbital elements. We are using the HARPS spectrograph to conduct our survey of ≈850 nearby solar-type stars, and in the course of the past nine years we have monitored the radial velocity of HD 103774, HD 109271, and BD-061339. In this work we present the detection of five planets orbiting these stars, with msin   (i) between 0.6 and 7 Neptune masses, four of which are in two multiple systems, comprising one super-Earth and one planet within the habitable zone of a late-type dwarf. Although for strategic reasons we chose efficiency over precision in this survey, we have the capability to detect planets down to the Neptune and super-Earth mass range as well as multiple systems, provided that enough data points are made available.

What is ‘wood’ – An anatomical re-definition

The technical definition of ‘wood’ is well accepted, but its botanical understanding remains vague. Different degrees and amounts of lignification in plants and their imprecise description, together with a conceptually doubtful life form catalog including trees, shrubs and herbs further complicate our understanding of ‘wood’. Here, we use permanent micro sections to demonstrate that the xylem and bark of terrestrial plants can vary from one tissue with a few lignified cells to an almost fully lignified tissue. This universal principle of plant growth and stabilization, accounting for all taxonomic units within vascular plants, suggests that the classical life form separation into herbs, shrubs and trees is not valid. An anatomical-based differentiation between ‘wood’, ‘woody’ and ‘woodiness’ is also only meaningful if supplemented by insight on the particular plant section and its lignified proportion. We therefore recommend utilizing the botanically more neutral term ‘stem anatomy’ instead of ‘wood anatomy’, which further implies integration of the xylem and bark of all terrestrial plants. Since dendrochronology considers shrubs, dwarf shrubs and perennial herbs in addition to trees, its semantic expansion toward ‘xylemchronology’ might be worthwhile considering.

Semi-dwarfism and lodging tolerance in tef (Eragrostis tef) is linked to a mutation in the α-Tubulin 1 gene

Genetic improvement of native crops is a new and promising strategy to combat hunger in the developing world. Tef is the major staple food crop for approximately 50 million people in Ethiopia. As an indigenous cereal, it is well adapted to diverse climatic and soil conditions; however, its productivity is extremely low mainly due to susceptibility to lodging. Tef has a tall and weak stem, liable to lodge (or fall over), which is aggravated by wind, rain, or application of nitrogen fertilizer. To circumvent this problem, the first semi-dwarf lodging-tolerant tef line, called kegne, was developed from an ethyl methanesulphonate (EMS)-mutagenized population. The response of kegne to microtubule-depolymerizing and -stabilizing drugs, as well as subsequent gene sequencing and segregation analysis, suggests that a defect in the α-Tubulin gene is functionally and genetically tightly linked to the kegne phenotype. In diploid species such as rice, homozygous mutations in α-Tubulin genes result in extreme dwarfism and weak stems. In the allotetraploid tef, only one homeologue is mutated, and the presence of the second intact α-Tubulin gene copy confers the agriculturally beneficial semi-dwarf and lodging-tolerant phenotype. Introgression of kegne into locally adapted and popular tef cultivars in Ethiopia will increase the lodging tolerance in the tef germplasm and, as a result, will improve the productivity of this valuable crop.

Are We Sims? How Computer Simulations Represent and What this Means for the Simulation Argument

N. Bostrom’s simulation argument and two additional assumptions imply that we are likely to live in a computer simulation. The argument is based upon the following assumption about the workings of realistic brain simulations: The hardware of a computer on which a brain simulation is run bears a close analogy to the brain itself. To inquire whether this is so, I analyze how computer simulations trace processes in their targets. I describe simulations as fictional, mathematical, pictorial, and material models. Even though the computer hardware does provide a material model of the target, this does not suffice to underwrite the simulation argument because the ways in which parts of the computer hardware interact during simulations do not resemble the ways in which neurons interact in the brain. Further, there are computer simulations of all kinds of systems, and it would be unreasonable to infer that some computers display consciousness just because they simulate brains rather than, say, galaxies.

The Inverted Phantom Giant

In his famous children’s book, “Jim Button and Luke the Engine Driver”, Michael Ende describes a curious character: A phantom giant. Clothed in rags and with a long beard, the phantom giant appears enormous from far away, but shrinks to normal size as one gets closer. Most people avoid the poor creature, but the ones that dare approach it encounter a gentle, lonely being called Mr. Tur Tur. Chemical ecology is just the opposite of Mr. Tur Tur: A phantom dwarf. Or, in other words, an inverted phantom giant. From a distance, chemical ecology appears like a slightly odd, marginal section of biology and chemistry. But, as the interested scholar approaches, it starts growing and very quickly reaches gigantic dimensions, because all life is explained by chemistry, and all biological chemistry is guided by ecological principles. Herein lies the difficulty with chemical ecology: As it is not perceived well by biologists and chemists, few approach it to understand its significance, and the ones that do find themselves in front of a giant that defies their attempts to define and contain it. This is where the Journal of Chemical Ecology comes in: It invites us to take a closer look at an underestimated discipline and supports us to explore it and deal with its multidimensionality through the promotion of knowledge and methods. These services are unique and make the journal stand out of the crowd of scientific journals. Writing children’s books has become difficult in the era of information technology. And, so has the job of the Journal of Chemical Ecology. Young scientists gather information through accessible, dynamic websites and social platforms. They want articles that are available through a single mouse click, anywhere, anytime. They prefer advanced interactive hypertext protocols over clumsy pdf files. They care about transparency, non-profit and open access just as much as about traditional journal properties. In my view, reaching “the kids” is the major challenge of the Journal over the next years. Promoting an inverted phantom giant in the 21st century requires a combination of high-quality information and boosted visibility. In Michael Ende’s book, Jim and Luke follow exactly this strategy with Mr. Tur Tur: They become friends and offer him a job as a living lighthouse to protect their small island. They combine a quality relationship with high visibility, et voilà, the story ends well! I am looking forward to seeing if the Journal of Chemical Ecology will follow a similar path to reach the next generation of biologists and chemists. If yes, there is a good chance that in 40 years from now, somebody will write a laudation and refer to another famous book by Michael Ende: “The Neverending Story”.

A nearby M Star with tree Transitting Supter-Earths Discovered by K2

Small, cool planets represent the typical end-products of planetary formation. Studying the architectures of these systems, measuring planet masses and radii, and observing these planets' atmospheres during transit directly informs theories of planet assembly, migration, and evolution. Here we report the discovery of three small planets orbiting a bright (K-s = 8.6 mag) M0 dwarf using data collected as part of K2, the new ecliptic survey using the repurposed Kepler spacecraft. Stellar spectroscopy and K2 photometry indicate that the system hosts three transiting planets with radii 1.5-2.1 R-circle plus, straddling the transition region between rocky and increasingly volatile-dominated compositions. With orbital periods of 10-45 days the planets receive just 1.5-10x the flux incident on Earth, making these some of the coolest small planets known orbiting a nearby star; planet d is located near the inner edge of the system's habitable zone. The bright, low-mass star makes this system an excellent laboratory to determine the planets' masses via Doppler spectroscopy and to constrain their atmospheric compositions via transit spectroscopy. This discovery demonstrates the ability of K2 and future space-based transit searches to find many fascinating objects of interest.

From stellar to planetary composition: Galactic chemical evolution of Mg/Si mineralogical ratio

Aims. The main goal of this work is to study element ratios that are important for the formation of planets of different masses. Methods. We study potential correlations between the existence of planetary companions and the relative elemental abundances of their host stars. We use a large sample of FGK-type dwarf stars for which precise Mg, Si, and Fe abundances have been derived using HARPS high-resolution and high-quality data. Results. A first analysis of the data suggests that low-mass planet host stars show higher [Mg/Si] ratios, while giant planet hosts present [Mg/Si] that is lower than field stars. However, we found that the [Mg/Si] ratio significantly depends on metallicity through Galactic chemical evolution. After removing the Galactic evolution trend only the difference in the [Mg/Si] elemental ratio between low-mass planet hosts and non-hosts was present in a significant way. These results suggest that low-mass planets are more prevalent around stars with high [Mg/Si]. Conclusions. Our results demonstrate the importance of Galactic chemical evolution and indicate that it may play an important role in the planetary internal structure and composition. The results also show that abundance ratios may be a very relevant issue for our understanding of planet formation and evolution.

Gibberellin Deficiency Confers Both Lodging and Drought Tolerance in Small Cereals

Tef [Eragrostis tef (Zucc.) Trotter] and finger millet [Eleusine coracana Gaertn] are staple cereal crops in Africa and Asia with several desirable agronomic and nutritional properties. Tef is becoming a life-style crop as it is gluten-free while finger millet has a low glycemic index which makes it an ideal food for diabetic patients. However, both tef and finger millet have extremely low grain yields mainly due to moisture scarcity and susceptibility of the plants to lodging. In this study, the effects of gibberellic acid (GA) inhibitors particularly paclobutrazol (PBZ) on diverse physiological and yield-related parameters were investigated and compared to GA mutants in rice (Oryza sativa L.). The application of PBZ to tef and finger millet significantly reduced the plant height and increased lodging tolerance. Remarkably, PBZ also enhanced the tolerance of both tef and finger millet to moisture deficit. Under moisture scarcity, tef plants treated with PBZ did not exhibit drought-related symptoms and their stomatal conductance was unaltered, leading to higher shoot biomass and grain yield. Semi-dwarf rice mutants altered in GA biosynthesis, were also shown to have improved tolerance to dehydration. The combination of traits (drought tolerance, lodging tolerance and increased yield) that we found in plants with altered GA pathway is of importance to breeders who would otherwise rely on extensive crossing to introgress each trait individually. The key role played by PBZ in the tolerance to both lodging and drought calls for further studies using mutants in the GA biosynthesis pathway in order to obtain candidate lines which can be incorporated into crop-breeding programs to create lodging tolerant and climate-smart crops.

Conditional expression of Sry, and Wnt4 by gene-targeting: Studies in sexual and skeletal development

Sry and Wnt4 cDNAs were individually introduced into the ubiquitously-expressed Rosa26 ( R26) locus by gene targeting in embryonic stem (ES) cells to create a conditional gene expression system in mice. In the targeted alleles, expression of these cDNAs should be blocked by a neomycin resistance selection cassette that is flanked by loxP sites. Transgene expression should be activated after the blocking cassette is deleted by Cre recombinase. ^ To test this conditional expression system, I have bred R26-stop- Sry and R26-stop-Wnt4 heterozygotes with a MisRII-Cre mouse line that expresses Cre in the gonads of both sexes. Analysis of these two types of bigenic heterozygotes indicated that their gonads developed normally like those of wild types. However, one XX R26-Sry/R26-Sry; MisR2-Cre/+ showed epididymis-like structures resembling those of males. In contrast, only normal phenotypes were observed in XY R26-Wnt4/R26-Wnt4; MisR2-Cre /+ mice. To interpret these results, I have tested for Cre recombinase activity by Southern blot and transcription of the Sry and Wnt4 transgenes by RT-PCR. Results showed that bigenic mutants had insufficient activation of the transgenes in their gonads at E12.5 and E13.5. Therefore, the failure to observe mutant phenotypes may have resulted from low activity of MisR2-Cre recombination at the appropriate time. ^ Col2a1-Cre transgenic mice express Cre in differentiating chondrocytes. R26-Wnt4; Col2a1-Cre bigenic heterozygous mice were found to exhibit a dramatic alteration in growth presumably caused by Wnt4 overexpression during chondrogenesis. R26-Wnt4; Col2a1-Cre mice exhibited dwarfism beginning approximately 10 days after birth. In addition, they also had craniofacial abnormalities, and had delayed ossification of the lumbar vertebrate and pelvic bones. Histological analysis of the growth plates of R26-Wnt4; Col2a1-Cre mice revealed less structural organization and a delay in onset of the primary and secondary ossification centers. Molecular studies confirmed that overexpression of Wnt4 causes decreased proliferation and early maturation of chondrocytes. In addition, R26-Wnt4; Col2a1-Cre mice had decreased expression of vascular endothelial growth factor (VEGF), suggesting that defects in vascularization may contribute to the dwarf phenotype. Finally, 9-month-old R26-Wnt4; Col2a1-Cre mice had significantly more fat cells in the marrow cavities of their metaphysis long bones, implying that long-term overexpression of Wnt4may cause bone marrow pathologies. In conclusion, Wnt4 was activated by Col2a1-Cre recombinase and was overexpressed in the growth plate, resulting in aberrant proliferation and differentiation of chondrocytes, and ultimately leads to dwarfism in mice. ^

A sex difference in seasonal timing of birth in a livebearing fish

Sex differences in seasonal timing include differences in hatch- or birth-date distribution and differences in the timing of migration or maturation such as protandrous arrival timing (PAT), which is early male arrival at breeding sites. I describe a novel form of protandrous arrival timing, as a sex difference in birth-date distribution in a live-bearing fish (Dwarf Perch, Micrometrus minimus). In this species, birth coincides with arrival at breeding sites because newborn males are sexually active. A series of samples of pregnant females and young of year was collected in Tomales Bay, CA. I analyzed the daily age record in otoliths to estimate the conception date of broods and the age that young-of-year individuals were born. Males were born at a younger age than females, as indicated by the daily age record and also by the predominance of females in broods from which some young had already been born, which was a common occurrence in pregnant females with older embryos. Sex ratio of broods varied with conception date such that early-season broods were predominantly male, possibly as a result of temperature-dependent sex determination. The combined effects of the sex difference in age at birth and seasonal shift in sex ratio were to shift the mean birth date of males relative to females by five days. The most likely ultimate explanation for PAT in the Dwarf Perch is that it arises from exploitation (scramble) competition for mating opportunities among recently-born young-of-year males.

Roles of p38 mitogen-activated protein kinase pathway in the regulation of SOX9 activity and chondrogenesis

Sox9 is a master transcription factor in chondrocyte differentiation. Several lines of evidence suggest that the p38 mitogen-activated protein kinase (MAPK) pathway is involved in chondrocyte differentiation. In the present study, we examined the roles of p38 in the regulation of SOX9 activity and chondrogenesis. ^ COS7 cells were transfected with a SOX9 expression vector and 4x48-p89, a luciferase construction harboring four tandem copies of a SOX9-dependent 48-bp enhancer in Col2a1. Coexpression of MKK6EE, a constitutively active mutant of MKK6, a MAPKK that specifically activates p38, further increased the activity of the SOX9-dependent 48-bp enhancer about 5-fold, and SOX9 protein levels were not increased under these conditions. This increase in enhancer activity was not observed in a mutant enhancer construct harboring mutations that abolish SOX9 binding. These data strongly suggested that activation of the p38 pathway results in increased activity of SOX9. In addition, the increase of the activity of the SOX9-dependent 48-bp enhancer by MKK6EE was also observed in primary chondrocytes, and this increase was abolished by coexpression of a p38 phosphatase, MKP5, and p38 specific inhibitors. Furthermore, treatment of primary chondrocytes with p38 inhibitors decreased the expression of Col2a1, a downstream target of Sox9, without affecting Sox9 RNA levels, further supporting the hypothesis that p38 plays a role in regulating Sox9 activity in chondrocytes. ^ To further study the role of the p38 MAPK pathway in chondrogenesis, we generated transgenic mice that express MKK6EE in chondrocytes under the control of the Col2a1 promoter/intron regulatory sequences. These mice showed a dwarf phenotype characterized by reduced chondrocyte proliferation and a delay in the formation of primary and secondary ossification centers. Histological analysis using in situ hybridization showed reduced expression of Indian hedgehog, PTH/PTHrP receptor, cyclin D1 and increased expression of p21. In addition, consistent with the notion that Sox9 activity was increased in these mice, transgenic mice that express MKK6EE in chondrocytes showed phenotypes similar to those of mice that overexpress SOX9 in chondrocytes. Therefore, our study provides in vivo evidence for the role of p38 in chondrocyte differentiation and suggests that Sox9 is a downstream target of the p38 MAPK pathway. ^

Climate and soil characteristics and soil arthropod abundance on Anchorage, Signy and Falkland Islands

Over a 2-year study, we investigated the effect of environmental change on the diversity and abundance of soil arthropod communities (Acari and Collembola) in the Maritime Antarctic and the Falkland Islands. Open Top Chambers (OTCs), as used extensively in the framework of the northern boreal International Tundra Experiment (ITEX), were used to increase the temperature in contrasting communities on three islands along a latitudinal temperature gradient, ranging from the Falkland Islands (51°S, mean annual temperature 7.5 °C) to Signy Island (60°S, -2.3°C) and Anchorage Island (67°S, -3.8°C). At each island an open and a closed plant community were studied: lichen vs. moss at the Antarctic sites, and grass vs. dwarf shrub at the Falkland Islands. The OTCs raised the soil surface temperature during most months of the year. During the summer the level of warming achieved was 1.7 °C at the Falkland Islands, 0.7 °C at Signy Island, and 1.1 °C at Anchorage Island. The native arthropod community diversity decreased with increasing latitude. In contrast with this pattern, Collembola abundance in the closed vegetation (dwarf shrub or moss) communities increased by at least an order of magnitude from the Falkland Islands (9.0 +/- 2 x 10**3 ind./m**2) to Signy (3.3 +/- 8.0 x 10**4 ind./m**2) and Anchorage Island (3.1 +/- 0.82 x 10**5 ind./m**2). The abundance of Acari did not show a latitudinal trend. Abundance and diversity of Acari and Collembola were unaffected by the warming treatment on the Falkland Islands and Anchorage Island. However, after two seasons of experimental warming, the total abundance of Collembola decreased (p < 0.05) in the lichen community on Signy Island as a result of the population decline of the isotomid Cryptopygus antarcticus. In the same lichen community there was also a decline (p < 0.05) of the mesostigmatid predatory mite Gamasellus racovitzai, and a significant increase in the total number of Prostigmata. Overall, our data suggest that the consequences of an experimental temperature increase of 1-2°C, comparable to the magnitude currently seen through recent climate change in the Antarctic Peninsula region, on soil arthropod communities in this region may not be similar for each location but is most likely to be small and initially slow to develop.

(Table 1) Normalized difference vegetation index in control and warming plots, Abisco Research Station

Extreme winter warming events in the sub-Arctic have caused considerable vegetation damage due to rapid changes in temperature and loss of snow cover. The frequency of extreme weather is expected to increase due to climate change thereby increasing the potential for recurring vegetation damage in Arctic regions. Here we present data on vegetation recovery from one such natural event and multiple experimental simulations in the sub-Arctic using remote sensing, handheld passive proximal sensors and ground surveys. Normalized difference vegetation index (NDVI) recovered fast (2 years), from the 26% decline following one natural extreme winter warming event. Recovery was associated with declines in dead Empetrum nigrum (dominant dwarf shrub) from ground surveys. However, E. nigrum healthy leaf NDVI was also reduced (16%) following this winter warming event in experimental plots (both control and treatments), suggesting that non-obvious plant damage (i.e., physiological stress) had occurred in addition to the dead E. nigrum shoots that was considered responsible for the regional 26% NDVI decline. Plot and leaf level NDVI provided useful additional information that could not be obtained from vegetation surveys and regional remote sensing (MODIS) alone. The major damage of an extreme winter warming event appears to be relatively transitory. However, potential knock-on effects on higher trophic levels (e.g., rodents, reindeer, and bear) could be unpredictable and large. Repeated warming events year after year, which can be expected under winter climate warming, could result in damage that may take much longer to recover.

Soil characteristics and Collembola and Acari abundance in control and warming plots at Abisco Research Station

Extreme weather events can have negative impacts on species survival and community structure when surpassing lethal thresholds. Extreme winter warming events in the Arctic rapidly melt snow and expose ecosystems to unseasonably warm air (2-10 °C for 2-14 days), but returning to cold winter climate exposes the ecosystem to lower temperatures by the loss of insulating snow. Soil animals, which play an integral part in soil processes, may be very susceptible to such events depending on the intensity of soil warming and low temperatures following these events. We simulated week-long extreme winter warming events - using infrared heating lamps, alone or with soil warming cables - for two consecutive years in a sub-Arctic dwarf shrub heathland. Minimum temperatures were lower and freeze-thaw cycles were 2-11 times more frequent in treatment plots compared with control plots. Following the second event, Acari populations decreased by 39%; primarily driven by declines of Prostigmata (69%) and the Mesostigmatic nymphs (74%). A community-weighted vertical stratification shift occurred from smaller soil dwelling (eu-edaphic) Collembola species dominance to larger litter dwelling (hemi-edaphic) species dominance in the canopy-with-soil warming plots compared with controls. The most susceptible groups to these winter warming events were the smallest individuals (Prostigmata and eu-edaphic Collembola). This was not apparent from abundance data at the Collembola taxon level, indicating that life forms and species traits play a major role in community assembly following extreme events. The observed shift in soil community can cascade down to the micro-flora affecting plant productivity and mineralization rates. Short-term extreme weather events have the potential to shift community composition through trait composition with potentially large consequences for ecosystem development.