Three dimensional (3D) spatial metrics for objects

Landscape Ecology - The increasing availability of lidar data and structure from motion processing techniques is moving pattern metric research toward the development of three-dimensional (3D)...     

CRISPR-Cas Technology in Plant Science

CRISPR-Cas technology has raised considerable interest among plant scientists, both in basic science and in plant breeding. Presently, the generation of random mutations at a predetermined site of the genome is well mastered, just like the targeted insertion of transgenes, although both remain restricted to species or genotypes amenable for plant transformation. On the other hand, true genome editing, i.e. the deliberate replacement of one or several nucleotides of the genome in a predetermined fashion, is limited to some rather particular examples that generally concern genes allowing positive selection, for example tolerance to herbicides. Therefore, further technological developments are necessary to fully exploit the potential of genome editing in enlarging the gene pool beyond the natural variability available in a given species. In principle, the technology can be applied to any quality related, agronomical or ecological trait, under the condition of upstream knowledge on the genes to be targeted and the precise modifications necessary to improve alleles. Published proof of concepts concern a wide range of agronomical traits, the most frequent being disease resistance, herbicide tolerance and the biochemical composition of harvested products. The regulatory status of the plants obtained by CRISPR-Cas technology raises numerous questions, in particular with regard to the plants that carry in their genomes the punctual modifications caused by the presence of the Cas9 nuclease but not the nuclease itself. Without clarification by the competent authorities, CRISPR-Cas technology would continue to be a powerful tool in functional genomics, but its potential in plant breeding would remain untapped.     

Comparing mating designs to restore seed production of interspecific hybrids between Trifolium repens (white clover) and Trifolium uniflorum

Interspecific hybrids between Trifolium uniflorum and cultivated white clover (Trifolium repens) have highly useful characteristics for temperate pastoral systems derived from both parent species. However, the early hybrids (F₁ and BC₁) also have unacceptably poor seed production for commerce. This study analysed the basis for the poor seed production and investigated breeding strategies for overcoming the problem. The BC₁F₁ generation produced lower‐than‐expected numbers of heads per plant and seeds per floret. Backcrossing of selected hybrids to white clover corrected these deficiencies and created new variation. Seed numbers were also returned to near target levels by recurrent selection within the BC₁ generation. Thus, it was possible to retain a theoretical average of 25% of T. uniflorum genome and still achieve high seed production per plant. The BC₁F₂ and BC₂F₁ generations produced high seed numbers per plant, along with reasonable variation. Both of these second‐generation hybrid forms have high reproductive potential and should be the focus for the selection of the desired combinations of agronomic and seed production traits.     

System for quasi‐continuous simultaneous measurement of oxygen diffusion rate and redox potential in soil

Oxygen diffusion rate (ODR) and redox potential (E_H) are quantitative indices representing oxygen availability and redox status in soils, which is valuable information for better understanding causes and effects of soil aeration. Because these indices are spatially and temporally highly variable, continuous measurements and adequate numbers of repetitions are essential for accurate in situ monitoring. Here, we present a new, fully automated recording system for in situ measurements where ODR and E_H are measured at the same platinum electrode. The conflict between electrode polarization for ODR and the resulting biased E_H readings is solved by reducing the polarization time and introducing a recovery interval between two consecutive measurement cycles. The shorter polarization time ensures accurate E_H readings. It also results in moderately overestimated ODR readings, but this can be corrected before data analysis. The recovery interval restricts temporal resolution of the E_H‐ODR data pairs to 8 h. We illustrate the use of the system with measurements in a field experiment in Zürich, Switzerland. ODR curves at different depths ran roughly parallel to the corresponding curves of O₂ concentration in soil air but ODR was much more sensitive to precipitation. Low ODR was a necessary but not a sufficient condition for declining E_H. E_H ran parallel to O₂ concentration in soil air rather than to ODR. The fully automated system allows for time series of replicate measurements in multifactorial field studies with reasonable labor requirements. It may be particularly suitable for studies examining the effects of soil tillage, compaction, and irrigation, where structure‐related soil properties such as porosity, gas permeability, and soil aeration play a dominant role.     

Regional and local scale variations in soil organic carbon stocks in West Greenland

The soil organic carbon (SOC) pool of the Northern Hemisphere contains about half of the global SOC stored in soils. As the Arctic is exceptionally sensitive to global warming, temperature rise and prolonged summer lead to deeper thawing of permafrost‐affected soils and might contribute to increasing greenhouse gas emissions progressively. To assess the overall feedback of soil organic carbon stocks (SOCS) to global warming in permafrost‐affected regions the spatial variation in SOCS at different environmental scales is of great interest. However, sparse and unequally distributed soil data sets at various scales in such regions result in highly uncertain estimations of SOCS of the Northern Hemisphere and here particularly in Greenland. The objectives of this study are to compare and evaluate three controlling factors for SOCS distribution (vegetation, landscape, aspect) at two different scales (local, regional). The regional scale reflects the different environmental conditions between the two study areas at the coast and the ice margin. On the local scale, characteristics of each controlling factor in form of defined units (vegetation units, landscape units, aspect units) are used to describe the variation in the SOCS over short distances within each study area, where the variation in SOCS is high. On a regional scale, we investigate the variation in SOCS by comparing the same units between the study areas. The results show for both study areas that SOCS are with 8 kg m^?2 in the uppermost 25 cm and 16 kg m^?2 in the first 100 cm of the soil, i.e., 3 to 6 kg m^?2 (37.5%) higher than existing large scale estimations of SOCS in West Greenland. Our approach allows to rank the scale‐dependent importance of the controlling factors within and between the study areas. However, vegetation and aspect better explain variations in SOCS than landscape units. Therefore, we recommend vegetation and aspect for determining the variation in SOCS in West Greenland on both scales.     

Comparative proteomic analysis of mushroom cell wall proteins among the different developmental stages of Pleurotus tuber-regium

Cell wall proteins (CWPs) play a vital role in the development of the different morphological stages including mycelium, fruiting body, and sclerotium in mushrooms which are important human food sources. Using fractionation by detergents and reducing agents, mushroom cell wall fractions from the different developmental stages of Pleurotus tuber-regium (PTR) were prepared. Using one-dimensional gel electrophoresis coupled with LC-MS, there were 103, 91, and 48 noncovalently linked CWPs identified in the cell wall fractions of the PTR mycelium, fruiting body, and sclerotium, respectively. Comparing the CWPs in these cell wall fractions, 19 of them were in common, among which 17 belonged to the functional categories of translation, ribosomal structure, and biogenesis. This is the first study to provide important biochemical insights into the different developmental stages of PTR mediated by CWPs, and the identified CWPs helped to explain the morphological changes of PTR mushrooms during cultivation.     

Applicability of ground‐penetrating radar as a tool for nondestructive soil‐depth mapping on Pleistocene periglacial slope deposits

Soil depth plays a decisive role in determining soil properties in mountainous regions for ecological site assessment. To evaluate the use of ground‐penetrating radar (GPR) for fast and high‐resolution mapping within mountainous regions, we examined the possibilities and limitations of GPR to determine soil depth over bedrock and to delineate individual substrate layers formed during the Pleistocene in a periglacial environment (Pleistocene periglacial slope deposits, PPSD). Selected catenae in representative subregions of the study area (Dill catchment, SE Rhenish Massif, Germany) have been successfully mapped using GPR. A practicable method was developed using a 400 MHz antenna to reach a mean penetration depth of 1.5 m and to map different substrates and layers of PPSD based on calibrations of the GPR at soil pits along 12 catenae. Colluvium, the three types of PPSD layers, as well as the in situ bedrock could be distinguished in most sections of the GPR surveys. Characteristic GPR facies caused by intrinsic material properties of the different substrates, such as stone content and soil moisture content, could be distinguished in different geomorphologic and lithological settings. A layer‐based velocity distribution was determined for characteristic substrate layers at soil pits enabling us to considerably enhance the accuracy of soil‐depth prediction. Compared to traditionally surveyed soil profiles, our results demonstrate an accuracy of layer thickness surveying within a standard deviation of approx. 0.1 m. It is demonstrated that the combination of GPR with conventional soil‐pit mapping is an efficient and valid method to produce high‐resolution data of substrate distribution.