Challenges in imaging and predictive modeling of rhizosphere processes

Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes

Changes in soil and vegetation properties under different land uses in Northern Scandinavia

We studied changes in vegetation, soil microbiology and soil properties during a 3 years study in a Fennoscandia tundra. The test sites were located at the border between Norway and Finland, a region which is divided by a fence to different areas of land use by reindeer herding. The Norwegian site acts as winter pasture only, the Finnish site is under use all the year. Due to shifts of the fence some years ago, an area of recover was found. Reindeer grazing and trampling changed not only vegetation cover, mainly from lichen heaths in Norway to grass and shrub land at the Finnish side. This had also consequences on soil properties, the microbial community and soil respiration. Differences in these items, however, are not directly to changes in vegetation cover; more dangerous are trampled and probably highly grazed spots which show barren soils. Main effect to soil respiration is temperature, which shows significant higher levels at the Finnish side, which leads to higher evaporation, thus lower moisture and thereof reduced microbial activity

Diverse Structural Evolution at z > 1 in Cosmologically Simulated Galaxies

From mock Hubble Space Telescope images, we quantify non-parametric statistics of galaxy morphology, thereby predicting the emergence of relationships among stellar mass, star formation, and observed rest-frame optical structure at 1 < z < 3. We measure automated diagnostics of galaxy morphology in cosmological simulations of the formation of 22 central galaxies with 9.3 < log10 M_*/M_sun < 10.7. These high-spatial-resolution zoom-in calculations enable accurate modeling of the rest-frame UV and optical morphology. Even with small numbers of galaxies, we find that structural evolution is neither universal nor monotonic: galaxy interactions can trigger either bulge or disc formation, and optically bulge-dominated galaxies at this mass may not remain so forever. Simulated galaxies with M_* > 10^10 M_sun contain relatively more disc-dominated light profiles than those with lower mass, reflecting significant disc brightening in some haloes at 1 < z < 2. By this epoch, simulated galaxies with specific star formation rates below 10^-9.7 yr^-1 are more likely than normal star-formers to have a broader mix of structural types, especially at M_* > 10^10 M_sun. We analyze a cosmological major merger at z ~ 1.5 and find that the newly proposed MID morphology diagnostics trace later merger stages while G-M20 trace earlier ones. MID is sensitive also to clumpy star-forming discs. The observability time of typical MID-enhanced events in our simulation sample is less than 100 Myr. A larger sample of cosmological assembly histories may be required to calibrate such diagnostics in the face of their sensitivity to viewing angle, segmentation algorithm, and various phenomena such as clumpy star formation and minor mergers.Comment: 23 pages, 16 figures, MNRAS accepted versio

Specific lid-base contacts in the 26s proteasome control the conformational switching required for substrate degradation.

The 26S proteasome is essential for proteostasis and the regulation of vital processes through ATP-dependent degradation of ubiquitinated substrates. To accomplish the multi-step degradation process, the proteasomes regulatory particle, consisting of lid and base subcomplexes, undergoes major conformational changes whose origin is unknown. Investigating the Saccharomyces cerevisiae proteasome, we found that peripheral interactions between the lid subunit Rpn5 and the base AAA+ ATPase ring are important for stabilizing the substrate-engagement-competent state and coordinating the conformational switch to processing states upon substrate engagement. Disrupting these interactions perturbs the conformational equilibrium and interferes with degradation initiation, while later processing steps remain unaffected. Similar defects in early degradation steps are observed when eliminating hydrolysis in the ATPase subunit Rpt6, whose nucleotide state seems to control proteasome conformational transitions. These results provide important insight into interaction networks that coordinate conformational changes with various stages of degradation, and how modulators of conformational equilibria may influence substrate turnover

Dss1 is a 26S proteasome ubiquitin receptor

The ubiquitin-proteasome system is the major pathway for protein degradation in eukaryotic cells. Proteins to be degraded are conjugated to ubiquitin chains that act as recognition signals for the 26S proteasome. The proteasome subunits Rpn10 and Rpn13 are known to bind ubiquitin, but genetic and biochemical data suggest the existence of at least one other substrate receptor. Here, we show that the phylogenetically conserved proteasome subunit Dss1 (Sem1) binds ubiquitin chains linked by K63 and K48. Atomic resolution data show that Dss1 is disordered and binds ubiquitin by binding sites characterized by acidic and hydrophobic residues. The complementary binding region in ubiquitin is composed of a hydrophobic patch formed by I13, I44, and L69 flanked by two basic regions. Mutations in the ubiquitin-binding site of Dss1 cause growth defects and accumulation of ubiquitylated proteins

Discovering bright quasars at intermediate redshifts based on the optical/near-IR colors

Identifications of quasars at intermediate redshifts (2.2<z<3.5) are inefficient in most previous quasar surveys as their optical colors are similar to those of stars. The near-IR K-band excess technique has been suggested to overcome this difficulty. Our study also proposed to use optical/near-IR colors for selecting z<4 quasars. To this method, we selected 105 unidentified bright targets with i<18.5 from the quasar candidates of SDSS DR6 with both SDSS ugriz optical and UKIDSS YJHK near-IR photometric data, which satisfy our proposed Y-K/g-z criterion and have photometric redshifts between 2.2 and 3.5 estimated from the 9-band SDSS-UKIDSS data. 43 of them were observed with the 2.16m telescope of NAOC in 2012. 36 of them were identified as quasars at 2.1<z<3.4. High success rate of discovering these quasars in the SDSS spectroscopic surveyed area demonstrates the robustness of both the Y-K/g-z selection criterion and the photometric redshift estimation technique. We also used the above criterion to investigate the possible star contamination rate to the quasar candidates of SDSS DR6, and found that it is much higher in selecting 3<z<3.5 quasar candidates than selecting lower redshift ones (z<2.2). The significant improvement in the photometric redshift estimation by using the 9-band SDSS-UKIDSS data than using the 5-band SDSS data is demonstrated and a catalog of 7,727 unidentified quasar candidates with photometric redshifts between 2.2 and 3.5 is provided. We also tested the Y-K/g-z selection criterion with the SDSS-III/DR9 quasar catalog, and found 96.2% of 17,999 DR9 quasars with UKIDSS Y and K-band data satisfy our criterion. With some samples of red and type II quasars, we found that 88% and 96.5% of them can be selected by the Y-K/g-z criterion respectively, which supports that using the Y-K/g-z criterion we can efficiently select both unobscured and obscured quasars. (abridged)Comment: 32 pages, 7 figures, 4 tables, accepted to A